From 61598b193b5b39e822b8515947d14e8b363a2451 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Wed, 14 Dec 2022 09:56:05 -0500 Subject: [PATCH] Release Candidate 2022-12-14 --- obi.owl | 8769 ++- views/NIAID-GSC-BRC.owl | 24 +- views/obi-base.owl | 136736 +++++++++++++++++++++---------------- views/obi.obo | 1060 +- views/obi_core.owl | 23 +- 5 files changed, 87359 insertions(+), 59253 deletions(-) diff --git a/obi.owl b/obi.owl index 77e77a99..edd0ac72 100755 --- a/obi.owl +++ b/obi.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -80,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-07-11 + 2022-12-14 @@ -2239,7 +2239,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ has performer - performer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system) + A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. + OBI + OBI + The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). has performer @@ -2690,6 +2693,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + has function realized in + capable of + + + + @@ -4258,6 +4273,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) @@ -6243,12 +6259,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ cell - cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell - cell @@ -6453,7 +6467,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ B cell A lymphocyte of B lineage that is capable of B cell mediated immunity. - A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. B cell @@ -6477,11 +6490,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ neuron - neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. neuron - neuron @@ -6738,6 +6749,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + malignant cell + A neoplastic cell that is capable of entering a surrounding tissue + + malignant cell + + + + @@ -6786,6 +6809,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + peripheral blood mononuclear cell + A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. + + peripheral blood mononuclear cell + + + + @@ -6880,10 +6916,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - transcription, RNA-templated - The cellular synthesis of RNA on a template of RNA. + RNA-templated transcription + The synthesis of an RNA transcript from an RNA template. - transcription, RNA-templated + RNA-templated transcription @@ -7101,6 +7137,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + L-iditol 2-dehydrogenase activity + Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+. + + L-iditol 2-dehydrogenase activity + + + + @@ -7125,6 +7173,90 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + acyl-CoA oxidase activity + Catalysis of the reaction: acyl-CoA + O2 = trans-2,3-dehydroacyl-CoA + hydrogen peroxide. + + acyl-CoA oxidase activity + + + + + + + + + L-alanine:2-oxoglutarate aminotransferase activity + Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate. + + L-alanine:2-oxoglutarate aminotransferase activity + + + + + + + + + alkaline phosphatase activity + Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum. + + alkaline phosphatase activity + + + + + + + + + L-aspartate:2-oxoglutarate aminotransferase activity + Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate. + + L-aspartate:2-oxoglutarate aminotransferase activity + + + + + + + + + cholinesterase activity + Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion. + + cholinesterase activity + + + + + + + + + creatine kinase activity + Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). + + creatine kinase activity + + + + + + + + + glutamate dehydrogenase [NAD(P)+] activity + Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+. + + glutamate dehydrogenase [NAD(P)+] activity + + + + @@ -7137,6 +7269,42 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + isocitrate dehydrogenase [NAD(P)+] activity + Catalysis of the reaction: isocitrate + NAD(P)+ = 2-oxoglutarate + CO2 + NAD(P)H. + + isocitrate dehydrogenase [NAD(P)+] activity + + + + + + + + + lactate dehydrogenase activity + Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate. + + lactate dehydrogenase activity + + + + + + + + + ribonuclease activity + Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. + + ribonuclease activity + + + + @@ -7330,6 +7498,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 5'-nucleotidase activity + Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate. + + 5'-nucleotidase activity + + + + @@ -7390,6 +7570,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + galactosidase activity + Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative. + + galactosidase activity + + + + @@ -7402,6 +7594,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + amylase activity + Catalysis of the hydrolysis of amylose or an amylose derivative. + + amylase activity + + + + + + + + + beta-N-acetylglucosaminidase activity + Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides. + + beta-N-acetylglucosaminidase activity + + + + @@ -8351,6 +8567,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + D-glutamyltransferase activity + Catalysis of the reaction: L(or D)-glutamine + D-glutamyl-peptide = NH3 + 5-glutamyl-D-glutamyl-peptide. + + D-glutamyltransferase activity + + + + @@ -12799,10 +13027,23 @@ No imports + + + + + Metazoa + metazoans + multicellular animals + + Metazoa + + + + - + Bilateria Bilateria @@ -12935,7 +13176,6 @@ No imports Caenorhabditis elegans - roundworm Caenorhabditis elegans @@ -13075,7 +13315,6 @@ No imports Homo sapiens human human being - man Homo sapiens @@ -16253,7 +16492,7 @@ for now. - + @@ -18474,12 +18713,12 @@ that has_part some material entity is a material entity. If we add as equivalent - intra cellular electrophysiology recording assay + intracellular electrophysiology recording assay - An electrophysiology recording assay where the recording location of the electrode is intracellular + An electrophysiology assay where the recording location of the electrode is intracellular. Frank Gibson Frank Gibson - intra cellular electrophysiology recording assay + intracellular electrophysiology recording assay @@ -18621,7 +18860,7 @@ that has_part some material entity is a material entity. If we add as equivalent extracellular electrophysiology recording assay The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron - An electrophysiology recording assay where the recording location of the electrode is extracellular + An electrophysiology assay where the recording location of the electrode is extracellular. Frank Gibson Helen Parkinson Frank Gibson @@ -21646,6 +21885,15 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + @@ -23746,7 +23994,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -23807,7 +24055,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ pathogen challenge - A pathogen challenge is the administration of a live pathogenic organism to a host + The administration of a live pathogenic organism to a host. pathogen challenge @@ -25239,12 +25487,16 @@ http://en.wikipedia.org/wiki/Survival_rate - - transcription factor binding site + + obsolete transcription factor binding site SO:0000235 - PLace_holder for sequence ontology term - transcription factor binding site + + PLace_holder for sequence ontology term + https://github.com/obi-ontology/obi/issues/1553 + + obsolete transcription factor binding site + true @@ -26523,7 +26775,7 @@ placeholder record of missing knowledge A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. - a information content entity created to indicate that information about something is not available to the person recording it. + An information content entity created to indicate that information about something is not available to the person recording it. This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. Bjoern Peters @@ -35260,31 +35512,9 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - efficacy of epitope intervention experiment - An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism. + An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism. Bjoern Peters efficacy of in vivo intervention efficacy of epitope intervention experiment @@ -35378,7 +35608,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. Bjoern Peters - tumor burden after challenge + protection from tumor challenge epitope protection from tumor challenge experiment @@ -35444,7 +35674,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. Bjoern Peters - pathogen urden after infectious challenge + burden after infectious challenge epitope protection from infectious challenge experiment based on pathogen burden @@ -36646,13 +36876,47 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -36660,13 +36924,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response + in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. IEDB IEDB - antibody help|biological activity - biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response + antibody help|in vivo assay + in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response @@ -37193,13 +37457,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells - A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor production by T cells. + A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells @@ -37915,13 +38179,47 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -37929,13 +38227,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response + in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB - T cell help|biological activity - biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response + T cell help|in vivo assay + in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response @@ -39999,16 +40297,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + - - - - - - + + + + + + + + + + + + + + @@ -40016,7 +40322,22 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + + + + + + + + + + + + + + + + @@ -40024,6 +40345,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 + in vivo assay measuring T cell epitope specific tolerance induction An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. @@ -40826,19 +41148,54 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity @@ -41023,13 +41380,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells + cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells - A cytometric bead array assay that detects tumor necrosis factor production by T cells. + A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|cytometric bead array - cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells + cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells @@ -42302,25 +42659,59 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring epitope specific T cell killing - A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay. + An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB cytotoxicity|in vivo assay @@ -42902,14 +43293,40 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) + + + + + + + + + + + + + + + + + + + + + + + + + + - biological activity assay measuring epitope specific T cell activation + assay measuring epitope specific T cell activation A T cell epitope dependent biological activity assay that detects T cell activation. IEDB IEDB activation|biological activity - biological activity assay measuring epitope specific T cell activation + assay measuring epitope specific T cell activation @@ -43202,13 +43619,13 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - assay measuring epitope specific tumor necrosis factor production by T cells + assay measuring epitope specific tumor necrosis factor alpha production by T cells - An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production. + An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|biological activity - assay measuring epitope specific tumor necrosis factor production by T cells + assay measuring epitope specific tumor necrosis factor alpha production by T cells @@ -44177,15 +44594,15 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells + + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells - A reporter cell line analyte detection bioassay that detects tumor necrosis factor production by T cells. + A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|bioassay - cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells @@ -44695,21 +45112,49 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific disease exacerbation @@ -44855,33 +45300,65 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - - in vivo assay measuring T cell epitope specific protection from tumor challenge + + + in vivo assay measuring T cell epitope specific protection after tumor burden challenge - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. + An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden. IEDB IEDB tumor burden after challenge|in vivo assay - in vivo assay measuring T cell epitope specific protection from tumor challenge + in vivo assay measuring T cell epitope specific protection after tumor burden challenge @@ -44906,39 +45383,61 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + - + - - - + + + - - + + - - + + - + + in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. + An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden. IEDB IEDB pathogen burden after challenge|in vivo assay @@ -45203,29 +45702,56 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - biological activity assay measuring T cell epitope specific in vivo activity + assay measuring T cell epitope specific in vivo activity A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. IEDB IEDB in vivo activity|biological activity - biological activity assay measuring T cell epitope specific in vivo activity + assay measuring T cell epitope specific in vivo activity @@ -45419,25 +45945,72 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + in vivo assay measuring T cell epitope specific protection based on survival - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. + An in vivo assay measuring T cell epitope specific protection from other challenge using survival. IEDB IEDB survival from challenge|in vivo assay @@ -45544,27 +46117,61 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - biological activity assay measuring epitope specific T cell helper activity + + in vivo assay measuring epitope specific T cell helper activity A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. IEDB IEDB - helper response|biological activity - biological activity assay measuring epitope specific T cell helper activity + helper response|in vivo assay + in vivo assay measuring epitope specific T cell helper activity @@ -45946,21 +46553,53 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific treatment of disease @@ -51047,13 +51686,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + + + + + + + + + + + + + + + + + + + + - + + + + + + @@ -51061,13 +51724,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - biological activity assay measuring epitope specific Ig-mediated histamine release + assay measuring epitope specific Ig-mediated histamine release - A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release. + A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB histamine release|biological activity - biological activity assay measuring epitope specific Ig-mediated histamine release + assay measuring epitope specific Ig-mediated histamine release @@ -51082,18 +51745,28 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + + + + + + + + + + + - biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation + assay measuring epitope specific immunoglobulin-mediated antigen activation A B cell epitope dependent biological activity determination assay that detects antigen activation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB antigen activation|biological activity - biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation + assay measuring epitope specific immunoglobulin-mediated antigen activation @@ -51104,13 +51777,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + + + + + + + + + + + + + + + + + + + + - + + + + + + @@ -51118,13 +51815,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - biological activity assay measuring epitope specific complement-dependent cytotoxicity + assay measuring epitope specific complement-dependent cytotoxicity - A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity. + A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro . PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB complement-dependent cytotoxicity|biological activity - biological activity assay measuring epitope specific complement-dependent cytotoxicity + assay measuring epitope specific complement-dependent cytotoxicity @@ -51135,13 +51832,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -51149,13 +51870,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity + assay measuring epitope specific antibody-dependent cellular cytotoxicity - A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity. + A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB antibody-dependent cellular cytotoxicity|biological activity - biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity + assay measuring epitope specific antibody-dependent cellular cytotoxicity @@ -51163,30 +51884,35 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - + + + + + - + - - - - + + + + + + + + + - - - - - biological activity assay measuring epitope specific immunoglobulin-mediated neutralization + + + + assay measuring epitope specific immunoglobulin-mediated neutralization A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB neutralization |biological activity - biological activity assay measuring epitope specific immunoglobulin-mediated neutralization + assay measuring epitope specific immunoglobulin-mediated neutralization @@ -51197,13 +51923,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + + + + + + + + + + + + + + + + + + + + - + + + + + + @@ -51211,13 +51961,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - biological activity assay measuring epitope specific opsonization + assay measuring epitope specific opsonization - A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization. + A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro . PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB opsonization|biological activity - biological activity assay measuring epitope specific opsonization + assay measuring epitope specific opsonization @@ -53146,17 +53896,47 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -53177,16 +53957,24 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - + - - - - - - + + + + + + + + + + + + + + @@ -53194,13 +53982,29 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific tolerance induction @@ -53219,16 +54023,24 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - + - - - - - - + + + + + + + + + + + + + + @@ -53236,13 +54048,29 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific induction of hypersensitivity @@ -53261,13 +54089,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + + + + + + + + + + + + + + + + - + + + + + + @@ -53275,13 +54127,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - biological activity assay measuring epitope specific immune complex formation + assay measuring epitope specific immune complex formation - A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination. + A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB agglutination|biological activity - biological activity assay measuring epitope specific immune complex formation + assay measuring epitope specific immune complex formation @@ -53289,23 +54141,75 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection based on survival - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. + An in vivo assay measuring B cell epitope specific protection from other challenge using survival. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB survival from challenge|in vivo assay @@ -53320,21 +54224,53 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific treatment of disease @@ -53353,29 +54289,56 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - biological activity assay measuring B cell epitope specific in vivo activity + assay measuring B cell epitope specific in vivo activity A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB in vivo activity|biological activity - biological activity assay measuring B cell epitope specific in vivo activity + assay measuring B cell epitope specific in vivo activity @@ -53644,30 +54607,49 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - + + + + - + - - + + + + + + + - - - - biological activity assay measuring epitope specific activation of additional immune response in vitro + + + + + + + + + + + + + + + + + + + assay measuring epitope specific activation of additional immune response in vitro A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. IEDB IEDB secondary in vitro activity|biological activity - biological activity assay measuring epitope specific activation of additional immune response in vitro + assay measuring epitope specific activation of additional immune response in vitro @@ -53692,13 +54674,29 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - biological activity assay measuring epitope specific antigen inhibition of antibody activity + + + + + + + + + + + + + + + + + assay measuring epitope specific antigen inhibition of antibody activity A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. IEDB IEDB antibody activity inhibition|biological activity - biological activity assay measuring epitope specific antigen inhibition of antibody activity + assay measuring epitope specific antigen inhibition of antibody activity @@ -53839,21 +54837,49 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from challenge @@ -53872,21 +54898,49 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific disease exacerbation @@ -59980,7 +61034,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -60046,6 +61100,17 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten + + + + + + + + + + + @@ -65882,7 +66947,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -66007,7 +67072,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -66851,39 +67916,64 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - - - - + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. + An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden. IEDB IEDB pathogen burden after challenge|in vivo assay @@ -66895,33 +67985,68 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - - - - - - - - in vivo assay measuring B cell epitope specific protection from tumor challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection after tumor burden challenge - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. + An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden. IEDB IEDB tumor burden after challenge|in vivo assay - in vivo assay measuring B cell epitope specific protection from tumor challenge + in vivo assay measuring B cell epitope specific protection after tumor burden challenge @@ -67301,25 +68426,48 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro assay measuring epitope specific T cell killing - A T cell epitope specific killing assay that uses an in vitro cell killing assay. + An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. IEDB IEDB cytotoxicity|in vitro assay @@ -67628,16 +68776,48 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -67659,6 +68839,46 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro assay measuring epitope specific proliferation of T cells @@ -67712,21 +68932,49 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from challenge @@ -67743,13 +68991,45 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - in vitro assay measuring T cell epitope specific suppression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring T cell epitope specific suppression in vitro T cell epitope dependent biological activity assay that detects suppression of an in vitro response. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB suppression|in vitro assay - in vitro assay measuring T cell epitope specific suppression + assay measuring T cell epitope specific suppression in vitro @@ -68206,25 +69486,48 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells - A T cell epitope specific proliferation assay performed on cells in vitro that uses a CFSE assay. + A CFSE assay that detects T cell epitope specific proliferation in vitro. IEDB IEDB proliferation|CFSE @@ -72642,7 +73945,7 @@ https://www.doi.org/ exposure to environmental and workplace carcinogens history - A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. + An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. Chris Stoeckert, Helena Ellis OBIB NCI BBRB @@ -73657,7 +74960,7 @@ https://www.doi.org/ An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. Chris Stoeckert, Mathias Brochhausen MIABIS 2.0 - 920 + https://github.com/obi-ontology/obi/issues/920 MIABIS 2.0 defined population inclusion criterion @@ -75826,7 +77129,7 @@ https://www.doi.org/ An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen - #839 + https://github.com/obi-ontology/obi/issues/839 age group inclusion criterion @@ -75867,7 +77170,7 @@ https://www.doi.org/ An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process. Mathias Brochhausen - #840 + https://github.com/obi-ontology/obi/issues/840 use of medication inclusion criterion @@ -77462,16 +78765,47 @@ https://www.doi.org/ - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -77496,18 +78830,56 @@ https://www.doi.org/ - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -77530,18 +78902,56 @@ https://www.doi.org/ - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -77564,16 +78974,47 @@ https://www.doi.org/ - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -77598,16 +79039,47 @@ https://www.doi.org/ - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -77629,10 +79101,72 @@ https://www.doi.org/ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specfic T cells. + An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. IEDB IEDB pathogen burden after challenge after adoptive transfer|in vivo assay @@ -77644,10 +79178,72 @@ https://www.doi.org/ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specific antibodies or B cells. + An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. IEDB IEDB pathogen burden after challenge after adoptive transfer|in vivo assay @@ -77659,33 +79255,87 @@ https://www.doi.org/ - - - - - - - + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specfic T cells. + An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival. IEDB IEDB - survival from challenge after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival + survival from other challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival @@ -77693,32 +79343,87 @@ https://www.doi.org/ - - - - - - - + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specific antibodies or B cells. + An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. IEDB IEDB - survival from challenge after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + survival from other challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival @@ -77726,14 +79431,76 @@ https://www.doi.org/ - - in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specfic T cells. + An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden. IEDB IEDB tumor burden after challenge after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden @@ -77741,14 +79508,76 @@ https://www.doi.org/ - - in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specific antibodies or B cells. + An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden. IEDB IEDB tumor burden after challenge after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden @@ -77759,21 +79588,58 @@ https://www.doi.org/ - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells @@ -77792,21 +79658,58 @@ https://www.doi.org/ - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells @@ -78371,19 +80274,62 @@ https://www.doi.org/ - - - - - - + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells. @@ -78398,19 +80344,62 @@ https://www.doi.org/ - - - - - - + + + + - - + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells. @@ -78428,16 +80417,28 @@ https://www.doi.org/ - + + + + + - - - - - - + + + + + + + + + + + + + + @@ -78445,7 +80446,22 @@ https://www.doi.org/ - + + + + + + + + + + + + + + + + @@ -78468,26 +80484,69 @@ https://www.doi.org/ - - - - - - + + + + - - + + - - - - biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells. IEDB IEDB - antibody help after adoptive transfer|biological activity - biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells + antibody help after adoptive transfer|in vivo assay + assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells @@ -78495,26 +80554,69 @@ https://www.doi.org/ - - - - - - + + + + - - + + - - - - biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells. IEDB IEDB - T cell help after adoptive transfer|biological activity - biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells + T cell help after adoptive transfer|in vivo assay + assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells @@ -78525,16 +80627,28 @@ https://www.doi.org/ - + + + + + - - - - - - + + + + + + + + + + + + + + @@ -78542,7 +80656,22 @@ https://www.doi.org/ - + + + + + + + + + + + + + + + + @@ -78553,7 +80682,7 @@ https://www.doi.org/ in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells - A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay after adoptive transfer of epitope specfic T cells. + An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells. IEDB IEDB cytotoxicity after adoptive transfer|in vivo assay @@ -78656,13 +80785,56 @@ https://www.doi.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells. @@ -78677,13 +80849,56 @@ https://www.doi.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells. @@ -78701,16 +80916,47 @@ https://www.doi.org/ - + + + + + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -82484,7 +84730,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre catheter - A catheter left inside the body, either temporarily or permanently, may be referred to as an "indwelling catheter". + A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body. https://orcid.org/0000-0002-8844-9165 @@ -83069,13 +85315,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Mosquito Magnet trap + Mosquito Magnet Pro trap An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. John Judkins IRO:0000022 https://github.com/obi-ontology/obi/issues/1217 - Mosquito Magnet trap + Mosquito Magnet Pro trap @@ -83264,7 +85510,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment. Chris Stoeckert https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design - #1090 + https://github.com/obi-ontology/obi/issues/1090 population based design @@ -90621,7 +92867,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood microbiology datum - An organism identification assay that is the specified output of a blood microbiology assay. + An organism identification datum that is the specified output of a blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90663,7 +92909,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre feces microbiology datum - An organism identification assay that is the specified output of a feces microbiology assay. + An organism identification datum that is the specified output of a feces microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90705,7 +92951,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre urine microbiology datum - An organism identification assay that is the specified output of a urine microbiology assay. + An organism identification datum that is the specified output of a urine microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90747,7 +92993,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre induced sputum microbiology datum - An organism identification assay that is the specified output of an induced sputum microbiology assay. + An organism identification datum that is the specified output of an induced sputum microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90789,7 +93035,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cerebrospinal fluid microbiology datum - An organism identification assay that is the specified output of a cerebrospinal fluid microbiology assay. + An organism identification datum that is the specified output of a cerebrospinal fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90810,7 +93056,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre endotracheal aspirate assay datum - An organism identification assay that is the specified output of an endotracheal aspirate assay. + An organism identification datum that is the specified output of an endotracheal aspirate assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90831,7 +93077,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre endotracheal tube aspirate microbiology datum - An organism identification assay that is the specified output of an endotracheal tube aspirate microbiology assay. + An organism identification datum that is the specified output of an endotracheal tube aspirate microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90852,7 +93098,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre lung microbiology datum - An organism identification assay that is the specified output of a lung microbiology assay. + An organism identification datum that is the specified output of a lung microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90873,7 +93119,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre nasopharyngeal or oropharyngeal swab microbiology datum - An organism identification assay that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. + An organism identification datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90894,7 +93140,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre pleural fluid microbiology datum - An organism identification assay that is the specified output of a pleural fluid microbiology assay. + An organism identification datum that is the specified output of a pleural fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90915,7 +93161,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre umbilical cord blood assay datum - An organism identification assay that is the specified output of an umbilical cord blood assay. + An organism identification datum that is the specified output of an umbilical cord blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -90936,7 +93182,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre umbilical cord blood microbiology datum - An organism identification assay that is the specified output of an umbilical cord blood microbiology assay. + An organism identification datum that is the specified output of an umbilical cord blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -92755,13 +95001,15 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf - A processed material that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. + A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. John Judkins OBI, VEuPathDB + https://github.com/obi-ontology/obi/issues/1456 + VEuPathDB assay kit @@ -92983,7 +95231,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre placental blood microbiology datum - An organism identification assay that is the specified output of a placental blood microbiology assay. + An organism identification datum that is the specified output of a placental blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 @@ -93013,766 +95261,3882 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - - injection function - - The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - adapted from WEB: http://www.dictionary.net/injection - injection function + + + synaptosome preparation process + + A material component separation process where a synaptic terminal is isolated from a neuron by mild homogenization of nervous tissue under isotonic conditions and subsequent fractionation using differential and density gradient centrifugation. + Michelle Giglio + Suvarna Nadendla + url:https://en.wikipedia.org/wiki/Synaptosome + CFDE-GlyGen + synaptosome preparation process - + - - - - - - - - - - - - - - - - - - - - - - - - - - - Epstein Barr virus transformed B cell - PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. + + + + + + + + + Illumina HiSeq 1500 - A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch - Epstein Barr virus transformed B cell + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + HiSeq 1500 + https://jp.support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Illumina HiSeq 1500 - + - - - chimera + + + + + + + + + NextSeq 550 - An organism which contains cells or tissues with a different genotype - PERSON: Helen Parkinson - GROUP: OBI - chimera + A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.illumina.com/systems/sequencing-platforms/nextseq.html + https://github.com/obi-ontology/obi/issues/1546 + gEAR + NextSeq 550 - + - - - obsolete_anatomical entity - Tissue, organ, system, sperm, blood or body location (arm). - - An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' - Bjoern Peters - Philippe Rocca-Serra - Tina Boussard - MO - - obsolete_anatomical entity - true + + + + + + + + + Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 + + A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.agilent.com/cs/library/brochures/IBS-231%20genomics%20catalog%20mech%20FINAL.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 - + - - - - - - - - - - - - - + + - - - - - - - - - - - - + + - blood plasma specimen - PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. + Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray - a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. - 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. - PERSON: Maura Gasparetto - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - plasma - WEB: http://en.wikipedia.org/wiki/Blood_plasma - blood plasma specimen + A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.agilent.com/cs/library/brochures/5990-6928en_lo.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray - + - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - blood serum specimen - PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. + Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray - A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. - PERSON: Maura Gasparetto - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/Blood_plasma - blood serum specimen + A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.agilent.com/cs/library/usermanuals/public/G4140-90050_GeneExpression_TwoColor_6.9.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray - + - - - - - - - - - - - - - organism - animal - fungus - plant - virus - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism + + + + + + + + + Affymetrix Mouse Genome 430 2.0 Array + + A DNA microarray manufactured by Affymetrix, which includes complete coverage of the GeneChip Mouse Expression Set 430, for analysis of over 39,000 transcripts and variants from more than 34,000 well-characterized mouse genes and UniGene clusters, on a single array. The sequences for this array were selected from GenBank™, dbEST, and RefSeq., and sequence clusters cretaed from the UniGene database. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Mouse Genome 430 2.0 Array + https://www.thermofisher.com/order/catalog/product/900497 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Genome 430 2.0 Array - + - - - obsolete_immortal cell - a single Hela cell + + + + + + + + + Affymetrix Mouse Genome 430A 2.0 Array - a cell derived from a multicellular organism that has the potential to replicate indefinitely - PERSON: Bjoern Peters - GROUP: OBI Biomaterial Branch - - obsolete_immortal cell - true + A DNA microarray manufactured by Affymetrix for gene expression analysis focusing on approximately 14,000 well-characterized genes in the transcribed mouse genome using single-array cartridge. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Mouse Genome 430A 2.0 Array + https://www.thermofisher.com/order/catalog/product/900500TS?SID=srch-srp-900500TS + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Genome 430A 2.0 Array - + - - - obsolete_fragment derived from protein - the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme - - A material entity which is derived from a protein - PERSON: Bjoern Peters - GROUP: IEDB - - obsolete_fragment derived from protein - true + + + + + + + + + Affymetrix Mouse Gene 1.0 ST Array + + A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Mouse Gene 1.0 ST Array + https://www.thermofisher.com/order/catalog/product/901168 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Gene 1.0 ST Array - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - phosphate buffered saline solution - PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes. - - Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - PERSON: Tina Boussard - PBS buffer - WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline - phosphate buffered saline solution + Affymetrix Mouse Gene 2.1 ST Array + + A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA).To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Mouse Gene 2.1 ST Array + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fmouse_gene_array_datasheet.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Gene 2.1 ST Array - + - - - - - - - - - - - - - - specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. - - A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - PERSON: James Malone - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial Branch - - specimen + + + + + + + + + Affymetrix Rhesus Macaque Genome Array + + A DNA microarray manufactured by Affymetrix,which is a single-labeled high-density oligonucleotide array, designed to study gene expression in the rhesus animal model and to interrogate rhesus transcripts orthologous to the 3' end of human transcripts. The array consists of over 52,000 probe sets representing more than 20,000 genes, and several relevant viral organisms for studying host-disease immune response. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Rhesus Macaque Genome Array + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0017705_702023_RhesusArray_PI.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Rhesus Macaque Genome Array - + - - - obsolete_cell line cell + + + + + + + + + Affymetrix Human Transcriptome Array 2.0 - A material entity that represents generations of a primary culture. - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch - - obsolete_cell line cell - true + A DNA microarray manufactured by Affymetrix, to go beyond gene-level expression profiling to accurately detect all known transcript isoforms produced by a gene. The array design covers >245,000 coding transcripts, >40,000 non-coding transcripts and >339,000 probe sets covering exon-exon junctions, thus ensuring uniform coverage of the transcriptome. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Human Transcriptome Array 2.0 + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fhta_array_2_0_datasheet.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Human Transcriptome Array 2.0 - + - - - obsolete_immortal cell line culture + + + + + + + + + Affymetrix Human Genome U219 Array - A cell line that is expected to be capable of indefinite propagation in an vitro culture. - PERSON:Matthew Brush - immortal cell line sample - permanent cell line - PERSON:Matthew Brush - - - obsolete_immortal cell line culture - true + A DNA microarray manufactured by Affymetrix, which comprises more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + Applied Biosystems GeneChip PrimeView Human Gene Expression Array + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0017681_703036_GeneChipPrimeViewArray_PI.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Human Genome U219 Array - + - - - - - - - - + + - - + + - xenograft - Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world + Affymetrix Human Gene 2.0 ST Array - A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - xenotransplant - WEB: http://en.wikipedia.org/wiki/Xenograft - xenograft + A DNA microarray manufactured by Affymetrix, which provides the most accurate, sensitive, and comprehensive measurement of protein coding (mRNA) and long intergenic non-coding RNA (lincRNA) transcripts. The array design covers >33,500 coding transcripts and >11,000 lincRNA transcripts thus enabling researchers to understand whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Human Gene 2.0 ST Array + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fhugene_2_st_datasheet.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Human Gene 2.0 ST Array - + - - - - - - - - + + - - + + + Affymetrix Clariom S Assay, Human + + A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the human transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers , and to quickly assess changes in key genes and pathways. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.thermofisher.com/order/catalog/product/902926#1_1 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Clariom S Assay, Human + + + + + + + + - - + + - cultured cell population - A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). - -A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). + Affymetrix Clariom S Assay, Mouse - A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. - 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. - PERSON:Matthew Brush - cell culture sample - PERSON:Matthew Brush - The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. - cultured cell population + A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the mouse transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers, and to quickly assess changes in key genes and pathways. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.thermofisher.com/order/catalog/product/902931?SID=srch-srp-902931, + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Clariom S Assay, Mouse - + - - + + - - + + + Illumina HumanHT-12 V4.0 expression beadchip + + An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling and expression-based quantitative trait loci (eQTL) studies. This BeadChip contains 12 arrays, each featuring more than 48,000 probes, targeting more than 31,000 annotated genes, providing genome-wide coverage of well-characterized genes, gene candidates, and splice variants. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.illumina.com/documents/products/technotes/technote_humanht_12_imputation.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Illumina HumanHT-12 V4.0 expression beadchip + + + + + + + + - - + + + Illumina MouseRef-8 v2.0 beadchip + + An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling in the mouse.This Beadchip contains 8 microarrays, featuring more than 25,000 probes per array, derived from the NCBI RefSeq database and supplemented with MEEBO and RIKEN FANTOM2 content. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/arraykits/whole-genome-gene-expression/WGGEX_Direct_Hybridization_Assay_Guide_11322355_A.pdf, https://www.illumina.com/documents/products/datasheets/datasheet_gene_exp_analysis.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Illumina MouseRef-8 v2.0 beadchip + + + + + + + + - - 0 - + + - primary cultured cell population - Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 - cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) + Affymetrix Mouse Exon Junction Array - A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. - - - 2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.' - PERSON:Matthew Brush - primary cell culture - primary cell culture sample - PERSON:Matthew Brush - primary cultured cell population + A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the mouse transcriptome. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://academic.oup.com/bioinformatics/article/26/2/268/209989 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Exon Junction Array - - - - - - - 0 - - - - consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. - - + - - - obsolete_cell line - A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592. - He, Tong-Chuan, et al. Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512. - To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene. Note that common usage in the literature is often of the form a human colorectal cancer cell line, as seen above. But such references to studies in a line refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. + + + + + + + + + Affymetrix Human Exon Junction Array - A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). - PERSON:Matthew Brush - cell line sample - OBI-CLO Alignment Working Group (Spring 2013) - - - obsolete_cell line - true + A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the human transcriptome. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://academic.oup.com/bioinformatics/article/26/2/268/209989 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Human Exon Junction Array - + - - - cultured clonal cell population - cell cut -Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 + + + administering substance in vivo to cause disease - A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical. - PERSON: Susanna Sansone - PERSON:Matthew Brush - clonal cell culture sample - GROUP: OBI Biomaterial Branch - cultured clonal cell population + An administration of substance in vivo with the intention to induce disease in the organism. + IEDB + IEDB + administering substance in vivo to cause disease - + - - - screening library - PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] - - a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process? - PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application -change biomaterial to material in definition - PERSON: Bjoern Peters - GROUP: IEDB - 7/13/09: Need to clarify if this meets reagent role definition - screening library + + + administering substance in vivo to reduce or prevent disease + + An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. + IEDB + IEDB + administering substance in vivo to reduce or prevent disease - + - - + + + - + - + + + + + - - - - synthetic peptide - the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme + + peripheral blood mononuclear cell specimen - a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment - changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi). - Bjoern Peters - IEDB - PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application - original term: protein fragment split into synthetic polypeptide and fragment derived from protein -DS: Is this synthetic an oxymoron to the biomaterial? - synthetic peptide + A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. + Chris Stoeckert + Jie Zheng + PBMC specimen + http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell + peripheral blood mononuclear cell specimen - + - - + + - + - - - - + + + + + + + - - - - - - - organ section - A liver slice used in a perfusion experiment. -Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521 - - A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) - PERSON: Helen Parkinson - PERSON: Philippe Rocca-Serra - GROUP: CEBS - GROUP: OBI Biomaterial Branch - organ section + mid-upper arm circumference datum + + A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm. + The Mother and Child Health and Education Trust + mid-upper arm circumference datum - + - - + + - - + + + antigen specific antibodies assay datum + + A data item that is the specified output of an antigen specific antibodies assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + antigen specific antibodies assay datum + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - bronchial alveolar lavage - solution containing lung derived T cells, eosinophils, and TNFa. + antigen specific antibodies in blood assay - Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. - PERSON: Bjoern Peters - BAL - GROUP: IEDB - bronchial alveolar lavage + An antigen specific antibodies assay that has a blood specimen as evaluant. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + VEuPathDB + antigen specific antibodies in blood assay - + - - - obsolete_polymer + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + antigen specific antibodies in milk assay - A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - James Malone - Philippe Rocca-Serra - TERM: CHEBI:33839 - - obsolete_polymer - true + An antigen specific antibodies assay that has a milk specimen as evaluant. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + VEuPathDB + antigen specific antibodies in milk assay - + - - + + - - + + - glucose in solution - Glucose present in blood - - A scattered aggregate of glucose molecules in a liquid - PERSON: Jie Zheng - glucose molecules - glucose in solution + antigen specific antibodies in blood assay datum + + An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + antigen specific antibodies in blood assay datum - + - - + + + - - + + - - + + antigen specific antibodies in milk assay datum + + An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + antigen specific antibodies in milk assay datum + + + + + + + + - + - - - - - - - - - - - - + + - - - - - - - - data transformation - The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - - A planned process that produces output data from input data. - Elisabetta Manduchi - Helen Parkinson - James Malone - Melanie Courtot - Philippe Rocca-Serra - Richard Scheuermann - Ryan Brinkman - Tina Hernandez-Boussard - data analysis - data processing - Branch editors - - data transformation + enzymatic activity level assay + + An assay in which the level of catalytic activity of an enzyme is determined. + James A. Overton + enzymatic activity level assay - + - - - - - + + + - + + + + + + + + + + + + 5'-nucleotidase activity level assay + + An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample. + James A. Overton + 5'-nucleotidase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + alanine aminotransferase activity level assay + + An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample. + James A. Overton + alanine aminotransferase activity level assay + + + + + + + + + + + - - + + + + + + + - - - - - - - - geometric mean calculation + + + alkaline phosphatase activity level assay + An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample. + James A. Overton + alkaline phosphatase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + amylase activity level assay + + An enzymatic activity level assay that measures the activity of amylase in a sample. + James A. Overton + amylase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + aspartate aminotransferase activity level assay + + An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample. + James A. Overton + aspartate aminotransferase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + cholinesterase activity level assay + + An enzymatic activity level assay that measures the activity of cholinesterase in a sample. + James A. Overton + cholinesterase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + creatine kinase activity level assay + + An enzymatic activity level assay that measures the activity of creatine kinase in a sample. + James A. Overton + creatine kinase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + gamma-glutamyltransferase activity level assay + + An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample. + James A. Overton + gamma-glutamyltransferase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + glutamate dehydrogenase activity level assay + + An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample. + James A. Overton + glutamate dehydrogenase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + isocitrate dehydrogenase activity level assay + + An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample. + James A. Overton + isocitrate dehydrogenase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + lactate dehydrogenase activity level assay + + An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample. + James A. Overton + lactate dehydrogenase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + sorbitol dehydrogenase activity level assay + + An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. + James A. Overton + sorbitol dehydrogenase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + acyl-CoA oxidase activity level assay + + An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. + James A. Overton + acyl-CoA oxidase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + N-acetyl-beta-glucosaminidase activity level assay + + An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. + James A. Overton + N-acetyl-beta-glucosaminidase activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + ribonuclease activity level assay + + An enzymatic activity level assay that measures the activity of ribonuclease in a sample. + James A. Overton + ribonuclease activity level assay + + + + + + + + + + + + + + + + + + + + + + + + + galactosidase activity level assay + + An enzymatic activity level assay that measures the activity of galactosidase in a sample. + James A. Overton + galactosidase activity level assay + + + + + + + + + Mosquito Magnet Liberty Plus trap + + An arthropod trap that is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor. + VEuPathDB + https://github.com/obi-ontology/obi/issues/1523 + Mosquito Magnet Liberty Plus trap + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tumor challenge + + The administration of a malignant cell to a host. + Hector Guzman-Orozco + IEDB + tumor challenge + + + + + + + + + in vivo challenge + + The administration of a challenge to a live host. + Hector Guzman-Orozco + IEDB + in vivo challenge + + + + + + + + + epitope protection from infectious challenge experiment based on survival + + An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. + Hector Guzman-Orozco + survival after infectious challenge + IEDB + https://github.com/obi-ontology/obi/issues/1594 + epitope protection from infectious challenge experiment based on survival + + + + + + + + + epitope protection from tumor challenge experiment based on burden + + An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls. + Hector Guzman-Orozco + burden after tumor challenge + IEDB + https://github.com/obi-ontology/obi/issues/1594 + epitope protection from tumor challenge experiment based on burden + + + + + + + + + epitope protection from tumor challenge experiment based on survival + + An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. + Hector Guzman-Orozco + survival after tumor challenge + IEDB + https://github.com/obi-ontology/obi/issues/1594 + epitope protection from tumor challenge experiment based on survival + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from pathogen challenge + + An in vivo assay measuring T cell epitope specific protection from pathogen challenge. + IEDB + IEDB + protection from pathogen challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection from pathogen challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from tumor challenge + + An in vivo assay measuring T cell epitope specific protection from tumor challenge. + IEDB + IEDB + protection from tumor challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection from tumor challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from other challenge + + An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor. + IEDB + IEDB + protection from other challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection from other challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific survival after tumor challenge + + An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival. + IEDB + IEDB + survival from tumor challenge|in vivo assay + in vivo assay measuring T cell epitope specific survival after tumor challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific survival after pathogen challenge + + An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival. + IEDB + IEDB + survival from pathogen challenge|in vivo assay + in vivo assay measuring T cell epitope specific survival after pathogen challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from pathogen challenge + + An in vivo assay measuring B cell epitope specific protection from pathogen challenge. + IEDB + IEDB + protection from pathogen challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection from pathogen challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from tumor challenge + + An in vivo assay measuring B cell epitope specific protection from tumor challenge. + IEDB + IEDB + protection from tumor challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection from tumor challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from other challenge + + An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor. + IEDB + IEDB + protection from other challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection from other challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific survival after pathogen challenge + + An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival. + IEDB + IEDB + survival from pathogen challenge|in vivo assay + in vivo assay measuring B cell epitope specific survival after pathogen challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific survival after tumor challenge + + An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival. + IEDB + IEDB + survival from tumor challenge|in vivo assay + in vivo assay measuring B cell epitope specific survival after tumor challenge + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells + + An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from pathogen challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival. + IEDB + IEDB + survival after pathogen challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells + + An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells. + IEDB + IEDB + protection from tumor challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival. + IEDB + IEDB + survival after tumor challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells + + An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells. + IEDB + IEDB + protection from other challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from pathogen challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. + IEDB + IEDB + survival after pathogen challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from tumor challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. + IEDB + IEDB + survival after tumor challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from other challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + + + + + + + + Gram stain assay + + An organism identification assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall. + Gram-positive bacteria retain the violet stain whereas gram-negative bacteria do not. + John Judkins ORCID:0000-0001-6595-0902 + American Heritage Medical Dictionary + NCI + https://github.com/obi-ontology/obi/issues/1603 + Gram stain assay + + + + + + + + + + + + + + + cow-baited arthropod trap + + A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent. + John Judkins ORCID:0000-0001-6595-0902 + Sarah Kelly + https://github.com/obi-ontology/obi/issues/1602 + cow-baited arthropod trap + + + + + + + + + + + + + + + + + + + + + + + + lymph specimen + + A specimen that is derived from a portion of lymph collected from an organism. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + lymph specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + digestive tract specimen + + A specimen that is derived from part of a digestive tract. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + digestive tract specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific interleukin-25 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells. + IEDB + IEDB + IL-25 release|biological activity + assay measuring epitope specific interleukin-25 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells. + IEDB + IEDB + IL-25 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells + + A flow cytometry assay that detects interleukin-25 production by T cells. + IEDB + IEDB + IL-25 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-25 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells. + IEDB + IEDB + IL-25 release|ELISA + ELISA measuring epitope specific interleukin-25 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells. + IEDB + IEDB + TNF release|bioassay + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + + + + + + + + injection function + + The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + adapted from WEB: http://www.dictionary.net/injection + injection function + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Epstein Barr virus transformed B cell + PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. + + A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch + Epstein Barr virus transformed B cell + + + + + + + + + chimera + + An organism which contains cells or tissues with a different genotype + PERSON: Helen Parkinson + GROUP: OBI + chimera + + + + + + + + + obsolete_anatomical entity + Tissue, organ, system, sperm, blood or body location (arm). + + An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' + Bjoern Peters + Philippe Rocca-Serra + Tina Boussard + MO + + obsolete_anatomical entity + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood plasma specimen + PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. + + a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. + 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. + PERSON: Maura Gasparetto + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + plasma + WEB: http://en.wikipedia.org/wiki/Blood_plasma + blood plasma specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood serum specimen + PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. + + A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. + PERSON: Maura Gasparetto + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + WEB: http://en.wikipedia.org/wiki/Blood_plasma + blood serum specimen + + + + + + + + + + + + + + + + + + + organism + animal + fungus + plant + virus + + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI. + GROUP: OBI Biomaterial Branch + WEB: http://en.wikipedia.org/wiki/Organism + organism + + + + + + + + + obsolete_immortal cell + a single Hela cell + + a cell derived from a multicellular organism that has the potential to replicate indefinitely + PERSON: Bjoern Peters + GROUP: OBI Biomaterial Branch + + obsolete_immortal cell + true + + + + + + + + + obsolete_fragment derived from protein + the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme + + A material entity which is derived from a protein + PERSON: Bjoern Peters + GROUP: IEDB + + obsolete_fragment derived from protein + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + phosphate buffered saline solution + PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes. + + Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + PERSON: Tina Boussard + PBS buffer + WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline + phosphate buffered saline solution + + + + + + + + + + + + + + + + + + + + specimen + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + + A material entity that has the specimen role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch + + specimen + + + + + + + + + obsolete_cell line cell + + A material entity that represents generations of a primary culture. + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch + + obsolete_cell line cell + true + + + + + + + + + obsolete_immortal cell line culture + + A cell line that is expected to be capable of indefinite propagation in an vitro culture. + PERSON:Matthew Brush + immortal cell line sample + permanent cell line + PERSON:Matthew Brush + + + obsolete_immortal cell line culture + true + + + + + + + + + + + + + + + + + + + + + xenograft + Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world + + A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + xenotransplant + WEB: http://en.wikipedia.org/wiki/Xenograft + xenograft + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured cell population + A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). + +A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). + + A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. + 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. + PERSON:Matthew Brush + cell culture sample + PERSON:Matthew Brush + The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. + cultured cell population + + + + + + + + + + + + + + + + + + + + + + + + 0 + + + + primary cultured cell population + Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 + cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) + + A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. + + + 2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.' + PERSON:Matthew Brush + primary cell culture + primary cell culture sample + PERSON:Matthew Brush + primary cultured cell population + + + + + + + + 0 + + + + consider if we really want to be so strict here . . . ie maybe we we say that they have not been output from an 'establishing cell line' process, but in some cases a passage or two may be allowed for a primary culture. the establishing of a line requires some procedss that attains a degree of homogeneity in the culture. + + + + + + + + + obsolete_cell line + A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592. + He, Tong-Chuan, et al. Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512. - To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene. Note that common usage in the literature is often of the form a human colorectal cancer cell line, as seen above. But such references to studies in a line refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. + + A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). + PERSON:Matthew Brush + cell line sample + OBI-CLO Alignment Working Group (Spring 2013) + + + obsolete_cell line + true + + + + + + + + + cultured clonal cell population + cell cut +Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 + + A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical. + PERSON: Susanna Sansone + PERSON:Matthew Brush + clonal cell culture sample + GROUP: OBI Biomaterial Branch + cultured clonal cell population + + + + + + + + + screening library + PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] + + a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process? + PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application +change biomaterial to material in definition + PERSON: Bjoern Peters + GROUP: IEDB + 7/13/09: Need to clarify if this meets reagent role definition + screening library + + + + + + + + + + + + + + + + + + + + + synthetic peptide + the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme + + a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment + changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi). + Bjoern Peters + IEDB + PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application + original term: protein fragment split into synthetic polypeptide and fragment derived from protein +DS: Is this synthetic an oxymoron to the biomaterial? + synthetic peptide + + + + + + + + + + + + + + + + + + + + + + + + + + + + organ section + A liver slice used in a perfusion experiment. +Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521 + + A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) + PERSON: Helen Parkinson + PERSON: Philippe Rocca-Serra + GROUP: CEBS + GROUP: OBI Biomaterial Branch + organ section + + + + + + + + + + + + + + + + + + + + + bronchial alveolar lavage + solution containing lung derived T cells, eosinophils, and TNFa. + + Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space. + PERSON: Bjoern Peters + BAL + GROUP: IEDB + bronchial alveolar lavage + + + + + + + + + obsolete_polymer + + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. + James Malone + Philippe Rocca-Serra + TERM: CHEBI:33839 + + obsolete_polymer + true + + + + + + + + + + + + + + + glucose in solution + Glucose present in blood + + A scattered aggregate of glucose molecules in a liquid + PERSON: Jie Zheng + glucose molecules + glucose in solution + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + data transformation + The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + + A planned process that produces output data from input data. + Elisabetta Manduchi + Helen Parkinson + James Malone + Melanie Courtot + Philippe Rocca-Serra + Richard Scheuermann + Ryan Brinkman + Tina Hernandez-Boussard + data analysis + data processing + Branch editors + + data transformation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + geometric mean calculation + + A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). Mathias Brochhausen PERSON: Mathias Brochhausen A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). @@ -98206,7 +103570,7 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 curated information PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. - A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts. + An information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts. 2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions. 2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference Person:Bjoern Peters @@ -106587,38 +111951,38 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - - - - - - - - - + - + + + + + + + + + + + + - biological activity assay measuring epitope specific T cell killing + assay measuring epitope specific T cell killing A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. IEDB IEDB cytotoxicity|biological activity - biological activity assay measuring epitope specific T cell killing + assay measuring epitope specific T cell killing @@ -106629,24 +111993,23 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - - - - - - - - - + - + + + + + + + + + + + @@ -106654,13 +112017,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - biological activity assay measuring epitope specific proliferation of T cells + assay measuring epitope specific proliferation of T cells A T cell epitope dependent biological activity assay that detects T cell proliferation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB proliferation|biological activity - biological activity assay measuring epitope specific proliferation of T cells + assay measuring epitope specific proliferation of T cells @@ -106686,25 +112049,48 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 51 chromium assay measuring epitope specific T cell killing - A T cell epitope specific killing assay performed in vitro that uses a chromium release assay. + A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. IEDB IEDB cytotoxicity|51 chromium @@ -106912,13 +112298,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - ELISA measuring epitope specific tumor necrosis factor production by T cells + ELISA measuring epitope specific tumor necrosis factor alpha production by T cells - An enzyme-linked immunosorbent assay that detects tumor necrosis factor production by T cells. + An enzyme-linked immunosorbent assay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|ELISA - ELISA measuring epitope specific tumor necrosis factor production by T cells + ELISA measuring epitope specific tumor necrosis factor alpha production by T cells @@ -107204,294 +112590,520 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + + + ELISA measuring epitope specific interleukin-17 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|ELISA + ELISA measuring epitope specific interleukin-17 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-18 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|ELISA + ELISA measuring epitope specific interleukin-18 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-4 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-4 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells + + An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells + IEDB + IEDB + TNFa release|ELISPOT + ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-10 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-10 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-13 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-13 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells + + A flow cytometry assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ICS + intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells + + A flow cytometry assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells + + A flow cytometry assay that detects tumor necrosis factor alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|ICS + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells + + A flow cytometry assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells + + A flow cytometry assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - ELISA measuring epitope specific interleukin-17 production by T cells - - An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ELISA - ELISA measuring epitope specific interleukin-17 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ELISA measuring epitope specific interleukin-18 production by T cells - - An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ELISA - ELISA measuring epitope specific interleukin-18 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ELISPOT assay measuring epitope specific interleukin-4 production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells - An enzyme-linked immunospot assay that detects interleukin-4 production by T cells. + A flow cytometry assay that detects interleukin-17 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB - IL-4 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-4 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells - - An enzyme-linked immunospot assay that detects tumor necrosis factor production by T cells. - IEDB - IEDB - TNFa release|ELISPOT - ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells + IL-17 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells - + - + - - - - + + + - + - + - - + + - - - - - - - - ELISPOT assay measuring epitope specific interleukin-10 production by T cells - - An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-10 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - ELISPOT assay measuring epitope specific interleukin-13 production by T cells - - An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-13 production by T cells - - - - - - - - - - - + + - - - - - - - - - - - - - - - - + - - - - - - intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells - - A flow cytometry assay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ICS - intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells - - - - - - - - - - - - - - - - - - - - - - + @@ -107499,25 +113111,26 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells + + + MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex - A flow cytometry assay that detects interleukin-2 production by T cells. + A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB - IL-2 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells + qualitative binding|multimer/tetramer + MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex - + - + - + @@ -107526,7 +113139,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -107537,44 +113150,16 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - - - intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells - - A flow cytometry assay that detects tumor necrosis factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|ICS - intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells - - - - - - - - - - - - - - - - - - - - + + + + @@ -107582,26 +113167,26 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells + + + 3H-thymidine assay measuring epitope specific proliferation of T cells - A flow cytometry assay that detects interleukin-4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + A tritiated thymidine incorporation assay that detects T cell epitope specific proliferation in vitro. + IEDB IEDB - IL-4 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells + proliferation|3H-thymidine + 3H-thymidine assay measuring epitope specific proliferation of T cells - + - + - + @@ -107610,7 +113195,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -107621,181 +113206,28 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - - - intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells - - A flow cytometry assay that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells - - A flow cytometry assay that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex - - A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|multimer/tetramer - MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex - - - - - - - - - - - - - - - - - - - - - - - - - - - 3H-thymidine assay measuring epitope specific proliferation of T cells - - A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay. - IEDB - IEDB - proliferation|3H-thymidine - 3H-thymidine assay measuring epitope specific proliferation of T cells - - - - - - - - - - - - - - - - - - - - + BrdU assay measuring epitope specific proliferation of T cells - A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay. + A BrdU incorporation assay that detects T cell epitope specific proliferation in vitro. IEDB IEDB proliferation|BrdU @@ -136939,12 +142371,24 @@ realizes some 'host of immune response role' + + + + + TF_binding_site + A DNA site where a transcription factor binds. + + TF_binding_site + + + + miRNA - Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. + Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. miRNA @@ -136999,6 +142443,18 @@ realizes some 'host of immune response role' + + + + + regulatory_region + A region of sequence that is involved in the control of a biological process. + + regulatory_region + + + + @@ -137496,7 +142952,7 @@ realizes some 'host of immune response role' pancreas - An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. pancreas @@ -137539,6 +142995,30 @@ realizes some 'host of immune response role' + + + + + arm + The part of the forelimb extending from the shoulder to the autopod[cjm]. + + arm + + + + + + + + + digestive tract + A tube extending from the mouth to the anus. + + digestive tract + + + + @@ -137947,6 +143427,18 @@ realizes some 'host of immune response role' + + + + + lymph + Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. + + lymph + + + + @@ -142733,9 +148225,6 @@ binary, and takes no temporal argument. - - - diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl index 44aedb81..c5c583c5 100644 --- a/views/NIAID-GSC-BRC.owl +++ b/views/NIAID-GSC-BRC.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg @@ -77,7 +77,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-07-11 + 2022-12-14 @@ -1545,6 +1545,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + @@ -1634,12 +1635,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ cell - cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell - cell @@ -1681,7 +1680,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ B cell A lymphocyte of B lineage that is capable of B cell mediated immunity. - A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. B cell @@ -2640,10 +2638,23 @@ Request that IAO either clarify these or change definitions not to use them + + + + Metazoa + metazoans + multicellular animals + + Metazoa + + + + - + Bilateria Bilateria @@ -2683,7 +2694,6 @@ Request that IAO either clarify these or change definitions not to use themHomo sapiens human human being - man Homo sapiens diff --git a/views/obi-base.owl b/views/obi-base.owl index a495f0de..3096f367 100644 --- a/views/obi-base.owl +++ b/views/obi-base.owl @@ -7,11 +7,13 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> + xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,7 +80,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-05-19 + 2022-12-14 @@ -100,159 +102,536 @@ + + + + Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. + Really of interest to developers only + BFO OWL specification label + + + + + + + + + Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 + Person:Alan Ruttenberg + Really of interest to developers only + BFO CLIF specification label + + + + + - + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + editor preferred label + editor preferred label + editor preferred term + editor preferred term + editor preferred term~editor preferred label + - + + example of usage + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + - + + in branch + An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. + GROUP:OBI + OBI_0000277 + in branch + - + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + has curation status + - + + definition + definition + textual definition + + The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + textual definition + - + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + + editor note + - + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + - + + alternative term + + An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + alternative term + - + + definition source + + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + - + + has obsolescence reason + Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + has obsolescence reason + - + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + + curator note + - + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item + - + + ontology term requester + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + ontology term requester + - + + is denotator type + Relates an class defined in an ontology, to the type of it's denotator + In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') + Alan Ruttenberg + is denotator type + - + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + - + + expand expression to + ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones + Chris Mungall + expand expression to + - + + expand assertion to + ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" + + A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. + Chris Mungall + expand assertion to + - + + first order logic expression + PERSON:Alan Ruttenberg + first order logic expression + - + + antisymmetric property + part_of antisymmetric property xsd:true + Use boolean value xsd:true to indicate that the property is an antisymmetric property + Alan Ruttenberg + antisymmetric property + - + + OBO foundry unique label + + An alternative name for a class or property which is unique across the OBO Foundry. + The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . + PERSON:Alan Ruttenberg + PERSON:Bjoern Peters + PERSON:Chris Mungall + PERSON:Melanie Courtot + GROUP:OBO Foundry <http://obofoundry.org/> + OBO foundry unique label + - + + has ID digit count + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) + Person:Alan Ruttenberg + has ID digit count + - + + has ID range allocated + Datatype: idrange:1 +Annotations: 'has ID range allocated to': "Chris Mungall" +EquivalentTo: xsd:integer[> 2151 , <= 2300] + + Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms + Person:Alan Ruttenberg + has ID range allocated to + - + + has ID policy for + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relating an ontology used to record id policy to the ontology namespace whose policy it manages + Person:Alan Ruttenberg + has ID policy for + - + + has ID prefix + Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> + Annotations: + 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" + 'has ID digit count' : 7, + rdfs:label "RO id policy" + 'has ID policy for': "RO" + Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. + Person:Alan Ruttenberg + has ID prefix + + + + + + + + elucidation + person:Alan Ruttenberg + Person:Barry Smith + Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms + + elucidation + + + + + + + + has associated axiom(nl) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom associated with a term expressed using natural language + + has associated axiom(nl) + + + + + + + + has associated axiom(fol) + Person:Alan Ruttenberg + Person:Alan Ruttenberg + An axiom expressed in first order logic using CLIF syntax + + has associated axiom(fol) + + + + + + + + is allocated id range + Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" + PERSON:Alan Ruttenberg + Add as annotation triples in the granting ontology + is allocated id range + + + + + + + + retired from use as of + relates a class of CRID to the date after which further instances should not be made, according to the central authority + In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp + Alan Ruttenberg + retired from use as of + + + + + + + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + + + + + + + + may be identical to + A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. + David Osumi-Sutherland + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + may be identical to + + + + + + + + scheduled for obsoletion on or after + Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. + Chris Mungall, Jie Zheng + https://github.com/geneontology/go-ontology/issues/15532 + https://github.com/information-artifact-ontology/ontology-metadata/issues/32 + GO ontology + scheduled for obsoletion on or after + + + + + + + + + has axiom id + Person:Alan Ruttenberg + Person:Alan Ruttenberg + A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI + + has axiom label + - + + term replaced by + + Use on obsolete terms, relating the term to another term that can be used as a substitute + Person:Alan Ruttenberg + Person:Alan Ruttenberg + Add as annotation triples in the granting ontology + term replaced by + + ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran @@ -269,6 +648,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng @@ -282,11 +662,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + IEDB alternative term - An alternative term used by the IEDB. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IEDB alternative term + An alternative term used by the IEDB. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IEDB alternative term @@ -295,20 +676,38 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + FGED alternative term - An alternative term used by the Functional Genomics Data (FGED) Society. - PERSON: Chris Stoeckert, Jie Zheng - Penn Group - FGED alternative term + An alternative term used by the Functional Genomics Data (FGED) Society. + PERSON: Chris Stoeckert, Jie Zheng + Penn Group + FGED alternative term + + + + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + temporal interpretation + https://oborel.github.io/obo-relations/temporal-semantics/ + + + + + Examples of a Contributor include a person, an + organisation, or a service. Typically, the name of a + Contributor should be used to indicate the entity. + An entity responsible for making contributions to the + content of the resource. + Contributor + Contributor @@ -316,7 +715,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Coverage will typically include spatial location (a place name + or geographic coordinates), temporal period (a period label, + date, or date range) or jurisdiction (such as a named + administrative entity). + Recommended best practice is to select a value from a + controlled vocabulary (for example, the Thesaurus of Geographic + Names [TGN]) and that, where appropriate, named places or time + periods be used in preference to numeric identifiers such as + sets of coordinates or date ranges. + The extent or scope of the content of the resource. + Coverage + Coverage @@ -324,7 +735,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Examples of a Creator include a person, an organisation, + or a service. Typically, the name of a Creator should + be used to indicate the entity. + An entity primarily responsible for making the content + of the resource. + Creator + Creator @@ -332,7 +750,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Typically, Date will be associated with the creation or + availability of the resource. Recommended best practice + for encoding the date value is defined in a profile of + ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. + A date associated with an event in the life cycle of the + resource. + Date + Date @@ -340,7 +766,13 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Description may include but is not limited to: an abstract, + table of contents, reference to a graphical representation + of content or a free-text account of the content. + An account of the content of the resource. + Description + Description @@ -348,7 +780,17 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Typically, Format may include the media-type or dimensions of + the resource. Format may be used to determine the software, + hardware or other equipment needed to display or operate the + resource. Examples of dimensions include size and duration. + Recommended best practice is to select a value from a + controlled vocabulary (for example, the list of Internet Media + Types [MIME] defining computer media formats). + The physical or digital manifestation of the resource. + Format + Format @@ -356,7 +798,17 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Recommended best practice is to identify the resource by means + of a string or number conforming to a formal identification + system. + Example formal identification systems include the Uniform + Resource Identifier (URI) (including the Uniform Resource + Locator (URL)), the Digital Object Identifier (DOI) and the + International Standard Book Number (ISBN). + An unambiguous reference to the resource within a given context. + Resource Identifier + Resource Identifier @@ -364,15 +816,37 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Recommended best practice is to use RFC 3066 [RFC3066], + which, in conjunction with ISO 639 [ISO639], defines two- + and three-letter primary language tags with optional + subtags. Examples include "en" or "eng" for English, + "akk" for Akkadian, and "en-GB" for English used in the + United Kingdom. + A language of the intellectual content of the resource. + Language + Language + + + + + + + Examples of a Publisher include a person, an organisation, + or a service. + Typically, the name of a Publisher should be used to + indicate the entity. + An entity responsible for making the resource available + Publisher + Publisher @@ -380,7 +854,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + Recommended best practice is to reference the resource by means + of a string or number conforming to a formal identification + system. + + A reference to a related resource. + Relation + Relation @@ -388,7 +870,20 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + Typically, a Rights element will contain a rights + management statement for the resource, or reference + a service providing such information. Rights information + often encompasses Intellectual Property Rights (IPR), + Copyright, and various Property Rights. + If the Rights element is absent, no assumptions can be made + about the status of these and other rights with respect to + the resource. + + Information about rights held in and over the resource. + Rights Management + Rights Management @@ -396,7 +891,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + The present resource may be derived from the Source resource + in whole or in part. Recommended best practice is to reference + the resource by means of a string or number conforming to a + formal identification system. + A reference to a resource from which the present resource + is derived. + Source + Source @@ -404,7 +907,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Typically, a Subject will be expressed as keywords, + key phrases or classification codes that describe a topic + of the resource. Recommended best practice is to select + a value from a controlled vocabulary or formal + classification scheme. + The topic of the content of the resource. + Subject and Keywords + Subject and Keywords @@ -412,7 +923,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + Typically, a Title will be a name by which the resource is + formally known. + + A name given to the resource. + Title + Title @@ -420,7 +938,16 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + Type includes terms describing general categories, functions, + genres, or aggregation levels for content. Recommended best + practice is to select a value from a controlled vocabulary + (for example, the DCMI Type Vocabulary [DCMITYPE]). To + describe the physical or digital manifestation of the + resource, use the Format element. + The nature or genre of the content of the resource. + Resource Type + Resource Type @@ -428,7 +955,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - Mark Miller + Mark Miller 2018-05-11T13:47:29Z @@ -440,15 +967,42 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + + + + + + + + + + + shorthand + + + + + + + + + + + label label @@ -466,6 +1020,24 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + + + + + + + + + + + + + - + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + @@ -534,67 +1123,432 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part - + + + + + realized in + this disease is realized in this disease course + this fragility is realized in this shattering + this investigator role is realized in this investigation + is realized by + realized_in + [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realized in + - + + + + realizes + this disease course realizes this disease + this investigation realizes this investigator role + this shattering realizes this fragility + to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + + realizes + - + + + + + + preceded by + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + preceded by + + + + + + + + + + + + precedes + precedes + - + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + - + + + + + has measurement unit label + + + + + + + + + The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. + +Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. + +c = pattern in the ink +b = paper + ink +r = friend + + c specifically denotes r =def +r is a portion of reality +& c is a particular quality +& c depends specifically on some independent continuant b +& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. + +Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. + +Case 1 +Memory trace as mark created when reading some description of some friend. The trace can denote. + +Case 2 +Pattern of ink arrayed on paper as mark when writing down a friend's name + +Case 3 +Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. + 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense + see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote + Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + obsolete_specifically denotes + true + - + + + This document is about information artifacts and their representations + + A (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + An information artifact IA mentions an entity E exactly when it has a component/part that denotes E + 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) + 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition + PERSON: Jonathan Rees + Person: Alan Ruttenberg + mentions + - + + + + + + A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. + A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically + 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. +g denotes r =def +r is a portion of reality +there is some c that is a concretization of g +every c that is a concretization of g specifically denotes r + person:Alan Ruttenberg + Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan + + denotes + + + + + + + + + see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote + + obsolete_materially denotes + true + - + + + + + + m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q + 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later + From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] + +This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. + +Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. +-- +From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] + +unit of measure is a quality, e.g. the length of a ruler. + +[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] + +[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] + +a represents b means either a denotes b or a describes + +describe: +a describes b means a is about b and a allows an inference of at least one quality of b + +We have had a long discussion about denotes versus describes. + From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. + +a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. + From the second meeting on IAO: + +An attempt at defining assay using Barry's "reliability" wording + +assay: +process and has_input some material entity +and has_output some information content entity +and which is such that instances of this process type reliably generate +outputs that describes the input. + This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. + +Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. + Alan Ruttenberg + is quality measurement of + + + + + + + + + + obsolete_describes + true + + + + + + + + + + obsolete_represents + true + + + + + + + + + + inverse of the relation 'denotes' + Person: Jie Zheng, Chris Stoeckert, Mike Conlon + + denoted by + - + + + + + + relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point + has coordinate unit label + - + + + + + + relates a process to a time-measurement-datum that represents the duration of the process + Person:Alan Ruttenberg + is duration of + + + + + + + + + inverse of the relation of is quality measurement of + 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship + Person:Alan Ruttenberg + is quality measured as + + + + + + + + + + + A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. + Person:Alan Ruttenberg + Person:Bjoern Peters + is quality specification of + + + + + + + + + inverse of the relation of is quality specification of + 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship + Person:Alan Ruttenberg + Person:Bjoern Peters + quality is specified as + + + + + + + + + + + + + relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken + Alan Ruttenberg + has time stamp + + + + + + + + + + + + + + + + + + + + + relates a time stamped measurement datum to the measurement datum that was measured + Alan Ruttenberg + has measurement datum + @@ -603,9 +1557,11 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + provides_service_consumer_with The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. + A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. - provides_service_consumer_with + provides_service_consumer_with @@ -615,13 +1571,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. + is_supported_by_data + The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. - The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process + The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI - Philly 2011 workshop - is_supported_by_data + Philly 2011 workshop + is_supported_by_data @@ -629,18 +1586,25 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + - has_specified_input + has_specified_input + has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. + 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Coutot + has_specified_input @@ -650,11 +1614,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - is_concretization_of - Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. - replaced by: http://purl.obolibrary.org/obo/BFO_0000058 - PERSON: Alan Ruttenburg - PERSON: Barry Smith + is_concretization_of + + Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. + replaced by: http://purl.obolibrary.org/obo/BFO_0000058 + PERSON: Alan Ruttenburg + PERSON: Barry Smith obsolete_is_concretization_of true @@ -667,12 +1632,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - is_specified_input_of + is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters + PERSON:Bjoern Peters is_specified_input_of @@ -682,11 +1647,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - is_concretized_as - Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. - replaced by: http://purl.obolibrary.org/obo/BFO_0000059 - PERSON: Alan Ruttenberg - PERSON: Barry Smith + is_concretized_as + + Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. + replaced by: http://purl.obolibrary.org/obo/BFO_0000059 + PERSON: Alan Ruttenberg + PERSON: Barry Smith obsolete_is_concretized_as true @@ -698,14 +1664,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - has_quality + has_quality - A relation between an entity and a quality. For types: E has_quality Q iff: + A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm] - replaced by: http://purl.obolibrary.org/obo/BFO_0000086 - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungall + replaced by: http://purl.obolibrary.org/obo/BFO_0000086 + GROUP:OBI:<http://obi.sourceforge.net> + PERSON: Chris Mungall obsolete_has_quality true @@ -716,16 +1682,23 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu + + + + + - has_specified_output + has_specified_output + has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot + PERSON: Bjoern Peters + PERSON: Larry Hunter + PERSON: Melanie Courtot + has_specified_output @@ -735,15 +1708,15 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - is_realized_by - - Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] - replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungall - executed_during - has_realization - is_realized_as + is_realized_by + + Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] + replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' + GROUP:OBI:<http://obi.sourceforge.net> + PERSON: Chris Mungall + executed_during + has_realization + is_realized_as obsolete_is_realized_by true @@ -755,10 +1728,11 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - obsoleted_has_specified_output_information + obsoleted_has_specified_output_information + A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data. PERSON: Alan Ruttenberg - PERSON: Frank Gibson + PERSON: Frank Gibson obsoleted_has_specified_output_information true @@ -780,6 +1754,7 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) + c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan @@ -794,13 +1769,13 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - has_function - heart has_function to-pump-blood + has_function + heart has_function to-pump-blood - Relation between an independent continuant and a function. - replaced by: http://purl.obolibrary.org/obo/BFO_0000085 - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungall + Relation between an independent continuant and a function. + replaced by: http://purl.obolibrary.org/obo/BFO_0000085 + GROUP:OBI:<http://obi.sourceforge.net> + PERSON: Chris Mungall obsolete_has_function true @@ -812,8 +1787,9 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - obsoleted_is_reagent_in + obsoleted_is_reagent_in some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole Alan Ruttenberg @@ -827,25 +1803,25 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - realizes - example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the + realizes + example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. - Relation between a process and a function, where the unfolding of the + Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm] - replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes' - GROUP:OBI:<http://obi.sourceforge.net> - PERSON: Chris Mungal - executes - has_function_part - involves_execution_of - is_realization_of + replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes' + GROUP:OBI:<http://obi.sourceforge.net> + PERSON: Chris Mungal + executes + has_function_part + involves_execution_of + is_realization_of obsolete_realizes true @@ -857,8 +1833,9 @@ instance level relation [GOC:cjm] - obsoleted_utilizes_reagent + obsoleted_utilizes_reagent see example_of_usage for is_reagent_in + Relationship between a protocol application and a substance that has role reagent that participates in the protocol application Alan Ruttenberg @@ -872,8 +1849,9 @@ instance level relation [GOC:cjm] - obsoleted_is_device_for + obsoleted_is_device_for some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay + Relationship between a device and a protocol application in which it participates Alan Ruttenberg @@ -886,13 +1864,20 @@ instance level relation [GOC:cjm] + + + + + - is_specified_output_of + is_specified_output_of + is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg - PERSON:Bjoern Peters + PERSON:Bjoern Peters + is_specified_output_of @@ -902,8 +1887,9 @@ instance level relation [GOC:cjm] - obsoleted_utilizes_device + obsoleted_utilizes_device see example_of_usage for is_device_for + Relationship between protocol application and an intrument in which it participates Alan Ruttenberg @@ -918,12 +1904,13 @@ instance level relation [GOC:cjm] - is_proxy_for + is_proxy_for position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity + A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be. A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the @@ -939,11 +1926,12 @@ level of radioactivity is_proxy_for level of toxicity - has specified input information + has specified input information + A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data. - PERSON: Frank Gibson + PERSON: Frank Gibson PERSON:Alan Ruttenberg - consumes data + consumes data obsoleted_has_specified_input_information true @@ -955,12 +1943,12 @@ level of radioactivity is_proxy_for level of toxicity - has_role + has_role - A relation between a continuant C and a role R. The reciprocal relation of role_of. - replaced by: http://purl.obolibrary.org/obo/BFO_0000087 - GROUP:OBI:<http://obi.sourceforge.net> - PERSON:Chris Mungal + A relation between a continuant C and a role R. The reciprocal relation of role_of. + replaced by: http://purl.obolibrary.org/obo/BFO_0000087 + GROUP:OBI:<http://obi.sourceforge.net> + PERSON:Chris Mungal obsolete_has_role true @@ -972,11 +1960,12 @@ level of radioactivity is_proxy_for level of toxicity - obsolete_results_from - 2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 + obsolete_results_from + + 2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 . Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys the - obsolete_results_from + obsolete_results_from true @@ -988,13 +1977,14 @@ level of radioactivity is_proxy_for level of toxicity - achieves_planned_objective - A cell sorting process achieves the objective specification 'material separation objective' - This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. - BP, AR, PPPB branch - PPPB branch derived - modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - achieves_planned_objective + achieves_planned_objective + A cell sorting process achieves the objective specification 'material separation objective' + + This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. + BP, AR, PPPB branch + PPPB branch derived + modified according to email thread from 1/23/09 in accordince with DT and PPPB branch + achieves_planned_objective @@ -1003,13 +1993,14 @@ level of radioactivity is_proxy_for level of toxicity - is_specified_information_output_of - A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation. - is replaced by has_specified_output_of - PERSON: James Malone - Editor + is_specified_information_output_of + + A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation. + is replaced by has_specified_output_of + PERSON: James Malone + Editor - obsoleted_is_specified_information_output_of + obsoleted_is_specified_information_output_of true @@ -1019,12 +2010,13 @@ level of radioactivity is_proxy_for level of toxicity - has grain - the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. + has grain + + the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg - PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 - has grain + PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 + has grain @@ -1033,11 +2025,12 @@ level of radioactivity is_proxy_for level of toxicity - obsoleted_is_specified_information_intput_of - Is the inverse relation of has_specfied_input_information - is replaced by is_specified_intput_of + obsoleted_is_specified_information_intput_of + + Is the inverse relation of has_specfied_input_information + is replaced by is_specified_intput_of - obsoleted_is_specified_information_intput_of + obsoleted_is_specified_information_intput_of true @@ -1047,7 +2040,8 @@ level of radioactivity is_proxy_for level of toxicity - is grain of + is grain of + A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole. JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic. PERSON: Alan Ruttenberg @@ -1061,12 +2055,13 @@ level of radioactivity is_proxy_for level of toxicity - provisions - A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use + provisions + + A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use 5/11/2020: A prior definition contained reference to transfer of ownership. ("A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship. - GROUP: Relations branch + GROUP: Relations branch supplies - provisions + provisions @@ -1083,14 +2078,14 @@ level of radioactivity is_proxy_for level of toxicity - has_supplier - - A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. - PERSON: Alan Rutternberg - PERSON: Cristian Cocos - PERSON: Frank Gibson - PERSON: Melanie Courtot - has_supplier + has_supplier + + A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. + PERSON: Alan Rutternberg + PERSON: Cristian Cocos + PERSON: Frank Gibson + PERSON: Melanie Courtot + has_supplier @@ -1100,12 +2095,12 @@ level of radioactivity is_proxy_for level of toxicity - objective_achieved_by + objective_achieved_by - This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. + This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI - objective_achieved_by + objective_achieved_by @@ -1123,16 +2118,17 @@ level of radioactivity is_proxy_for level of toxicity - is member of organization - Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. - 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population - JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. - Person:Alan Ruttenberg - Person:Helen Parkinson - Person:Alan Ruttenberg - Person:Helen Parkinson - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - is member of organization + is member of organization + + Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. + 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population + JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. + Person:Alan Ruttenberg + Person:Helen Parkinson + Person:Alan Ruttenberg + Person:Helen Parkinson + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + is member of organization @@ -1143,9 +2139,10 @@ level of radioactivity is_proxy_for level of toxicity - has category label + has category label + A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. - has category label + has category label @@ -1156,11 +2153,12 @@ level of radioactivity is_proxy_for level of toxicity - has disposition to bind - A relationship between two material entitites that each have disposition to form a complex with the other. - This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other - IEDB - has disposition to bind + has disposition to bind + + A relationship between two material entitites that each have disposition to form a complex with the other. + This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other + IEDB + has disposition to bind @@ -1177,10 +2175,12 @@ level of radioactivity is_proxy_for level of toxicity - Relating an organization to a legal person or organization. - See tracker: + has organization member + + Relating an organization to a legal person or organization. + See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 - Person: Jie Zheng + Person: Jie Zheng has organization member @@ -1191,6 +2191,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + specifies value of + A relation between a value specification and an entity which the specification is about. specifies value of @@ -1203,6 +2205,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton @@ -1234,25 +2237,45 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + has performer - performer relation covers the need to report on who performed a planned processed. it has to cover processes done by People or Devices (such as a robot controlled by software WF management system) + A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. + OBI + OBI + The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). has performer + + + + + has assay target context + + A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc. + Hector Guzman-Orozco + OBI + https://github.com/obi-ontology/obi/issues/1516 + has assay target context + + + + - process is result of - The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR - is a relationship between a process and a preceding occurrent that directly caused the later one to occur - IEDB - PERSON:Bjoern Peters - process is result of + process is result of + The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR + + is a relationship between a process and a preceding occurrent that directly caused the later one to occur + IEDB + PERSON:Bjoern Peters + process is result of @@ -1261,9 +2284,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - is_described_by + is_described_by + - obsolete_is_described_by + obsolete_is_described_by true @@ -1274,110 +2298,422 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - bound_to + bound_to + A relationship between two material entities that form a complex based on a selective, non-covalent interaction. The definition of this term is modeled after the Chebi:50967 and GO:0005488 terms. Further alignment of the logical definitions with those ontologies will require agreement on the placement of GO:molecular function in BFO among other things. OBI will retire this term once such an alignment is achieved as 'bound to' is not in the primary OBI scope. - bound_to + bound_to - + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + - + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + - + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + - + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + - + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + is concretized as + - + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). + An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). + A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + concretizes + - + + + + + this catalysis function is a function of this enzyme + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. + function_of + is function of + function of + + + + + + + + + + this red color is a quality of this apple + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + A quality inheres in its bearer at all times for which the quality exists. + is quality of + quality_of + quality of + - + + + + this investigator role is a role of this person + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. + is role of + role_of + role of + - + + + + + this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. + has_function + has function + - + + + + this apple has quality this red color + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. + has_quality + has quality + - + + + + + this person has role this investigator role (more colloquially: this person has this role of investigator) + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. + has_role + has role + + + + + + + + + + + + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition + + + + + + + + + disposition of + + + + derives from + this cell derives from this parent cell (cell division) + this nucleus derives from this parent nucleus (nuclear division) + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. + derives_from + + derives from + + + + + + + + this parent cell derives into this cell (cell division) + this parent nucleus derives into this nucleus (nuclear division) + + a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. + derives_into + derives into + + + + + + + + + + is location of + my head is the location of my brain + this cage is the location of this rat + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + location_of + + location of - + + + + + + + + + + + + + + + + + + + + + + + + + located in + my brain is located in my head + this rat is located in this cage + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus + Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + located_in + + http://www.obofoundry.org/ro/#OBO_REL:located_in + located in + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + + + + + + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. + + + + + + + + + the surface of my skin is a 2D boundary of my body + a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + 2D_boundary_of + boundary of + is 2D boundary of + is boundary of + + 2D boundary of + + + + + + + + + + my body has 2D boundary the surface of my skin + a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity + A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. + Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. + has boundary + has_2D_boundary + + has 2D boundary + - + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + - + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + has component + + + + + + + + + + + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + has function realized in + capable of + - + + + surrounded by + x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y + + surrounded by + @@ -1389,15 +2725,59 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + move to BFO? + Allen + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporal relation + + + + - + + + + + inverse of starts with + Chris Mungall + Allen + starts + + + + + + + + + + An organism that is a member of a population of organisms + is member of is a mereological relation between a item and a collection. + is member of + member part of + SIO + + member of + - + + + + has member is a mereological relation between a collection and an item. + SIO + + has member + @@ -1420,7 +2800,45 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + + + + has measurement value + + + + + + + + + + + has x coordinate value + + + + + + + + + + + has z coordinate value + + + + + + + + + + + has y coordinate value + @@ -1428,7 +2846,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - has_feature_value + has_feature_value + has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values. James Malone has_feature_value @@ -1442,6 +2861,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + has specified numeric value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. @@ -1456,6 +2876,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + has specified value + A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI @@ -1467,14 +2889,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + has representation 12th arrondissement of Paris - 20g + 20g I feel sick to my stomach every Tuesday 'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text. Further processing may enable the value to be represented in a component data structure such as an OBI value specification. - Damion Dooley - Mark Miller + Damion Dooley + Mark Miller 2019-07-14T07:05:50Z has representation @@ -1492,509 +2915,2598 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - + + + + + + + + + + + + + + + + + + + + + A planned process that has specified output a software product and that involves the creation of source code. + Mathias Brochhausen + William R. Hogan + http://en.wikipedia.org/wiki/Software_development + A planned process resulting in a software product involving the creation of source code. + software development - + - + + + + + + + + + + + + + + A measurement datum that is the output of counting. + Mathias Brochhausen + A measurement datum that is the output of counting. + count + - + - + + + + + + + + + + + + + + The planned process of finding the number of elements in a finite set of objects. + Mathias Brochhausen + http://en.wikipedia.org/wiki/Counting + The planned process of finding the number of elements in a finite set of objects. + counting + - + - + + + + + + + + + + + + + + + + + + + + + + + + + software source code version control repository + A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. + William R. Hogan + Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based + source code repository + - + - + + + + + + + + + + + + + + + + + + + + + + + + process of compiling software + A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. + William R. Hogan + It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). + Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. + compiling software + - + - + + + + + + + + + + + + + + creating a data set + A planned process that has a data set as its specified output. + William R. Hogan + data set creation + dataset creation + dataset creating + - + - + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + - + - + + + + + + + + + + continuant + Continuant + continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + - + - + + + + + + + + + occurrent + Occurrent + An entity that has temporal parts and that happens, unfolds or develops through time. + BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region + BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + occurrent + + + + + Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. + + per discussion with Barry Smith + + + + + Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. + + + + + + An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) + + + + + + Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) + + + + + + b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) + + + + + + (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] + + + + + + (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] + + - + - + + + + + ic + IndependentContinuant + a chair + a heart + a leg + a molecule + a spatial region + an atom + an orchestra. + an organism + the bottom right portion of a human torso + the interior of your mouth + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + independent continuant + + + + + For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) + + + + + + (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] + + + + + + (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] + + + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) + + - + - + + + A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. + obsolete dependent continuant + true + - + - + + + + + s-region + SpatialRegion + BFO 2 Reference: Spatial regions do not participate in processes. + Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. + A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) + All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + spatial region + + + + + Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. + + per discussion with Barry Smith + + + + + A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) + + + + + + All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) + + + + + + (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] + + + + + + (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] + + - + - + + + + + + t-region + TemporalRegion + Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional + A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) + All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) + Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) + (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] + (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] + (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] + + temporal region + + + + + Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional + + per discussion with Barry Smith + + + + + A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) + + + + + + All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) + + + + + + Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) + + + + + + (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] + + + + + + (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] + + + + + + (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] + + - + - + + + + 2d-s-region + TwoDimensionalSpatialRegion + an infinitely thin plane in space. + the surface of a sphere-shaped part of space + A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) + (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] + + two-dimensional spatial region + + + + + A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) + + + + + + (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] + + - - - + + + + + st-region + SpatiotemporalRegion + the spatiotemporal region occupied by a human life + the spatiotemporal region occupied by a process of cellular meiosis. + the spatiotemporal region occupied by the development of a cancer tumor + A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) + All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) + Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) + Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) + Every spatiotemporal region occupies_spatiotemporal_region itself. + Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) + (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] + (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] + (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] + (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] + (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] + + spatiotemporal region + + + + + A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) + + + + + + All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) + + + + + + Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) + + + + + + Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) + + + + + + Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) + + + + + + (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] + + + + + + (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] + + + + + + (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] + + + + + + (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] + + + + + + (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] + + - + - + + + process + Process + a process of cell-division, \ a beating of the heart + a process of meiosis + a process of sleeping + the course of a disease + the flight of a bird + the life of an organism + your process of aging. + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + process + + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + + + + + (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + + - + - + + + + disposition + Disposition + an atom of element X has the disposition to decay to an atom of element Y + certain people have a predisposition to colon cancer + children are innately disposed to categorize objects in certain ways. + the cell wall is disposed to filter chemicals in endocytosis and exocytosis + BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + disposition + + + + + b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) + + + + + + If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) + + + + + + (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] + + + + + + (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] + + - + - - - - - - - + + + + realizable + RealizableEntity + the disposition of this piece of metal to conduct electricity. + the disposition of your blood to coagulate + the function of your reproductive organs + the role of being a doctor + the role of this boundary to delineate where Utah and Colorado meet + A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + realizable entity + + + + To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) + + + + + + All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) + + + + + + (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] + + + + + + (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] + + - + - + + + + 0d-s-region + ZeroDimensionalSpatialRegion + A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) + (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] + + zero-dimensional spatial region + + + + + A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) + + + + + + (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] + + - + - + + + quality + Quality + quality + the ambient temperature of this portion of air + the color of a tomato + the length of the circumference of your waist + the mass of this piece of gold. + the shape of your nose + the shape of your nostril + + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + quality + + + + + a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) + + + + + + If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) + + + + + + (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] + + + + + + (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] + + - + - + + + + sdc + SpecificallyDependentContinuant + specifically dependent continuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) + + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] + + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + - + - + + + role + Role + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + the priest role + the role of a boundary to demarcate two neighboring administrative territories + the role of a building in serving as a military target + the role of a stone in marking a property boundary + the role of subject in a clinical trial + the student role + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + role + + + + + b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) + + + + + + (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] + + - + - + + + fiat-object + fiat-object-part + FiatObjectPart + or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 + the FMA:regional parts of an intact human body. + the Western hemisphere of the Earth + the division of the brain into regions + the division of the planet into hemispheres + the dorsal and ventral surfaces of the body + the upper and lower lobes of the left lung + BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions + b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) + (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] + + fiat object + fiat object part + + + + + b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) + + + + + + (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] + + - + - + + + + 1d-s-region + OneDimensionalSpatialRegion + an edge of a cube-shaped portion of space. + A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) + (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] + + one-dimensional spatial region + + + + + A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) + + + + + + (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] + + - + - + + + object-aggregate + ObjectAggregate + a collection of cells in a blood biobank. + a swarm of bees is an aggregate of members who are linked together through natural bonds + a symphony orchestra + an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) + defined by fiat: the aggregate of members of an organization + defined through physical attachment: the aggregate of atoms in a lump of granite + defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container + defined via attributive delimitations such as: the patients in this hospital + the aggregate of bearings in a constant velocity axle joint + the aggregate of blood cells in your body + the nitrogen atoms in the atmosphere + the restaurants in Palo Alto + your collection of Meissen ceramic plates. + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + object aggregate + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects + + + + + + ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. + + + + + + b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) + + + + + + (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] + + - - - - - + + + + + 3d-s-region + ThreeDimensionalSpatialRegion + a cube-shaped region of space + a sphere-shaped region of space, + A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) + (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] + + three-dimensional spatial region + + + + + A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) + + + + + + (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] + + + + + + + + + + site + Site + Manhattan Canyon) + a hole in the interior of a portion of cheese + a rabbit hole + an air traffic control region defined in the airspace above an airport + the Grand Canyon + the Piazza San Marco + the cockpit of an aircraft + the hold of a ship + the interior of a kangaroo pouch + the interior of the trunk of your car + the interior of your bedroom + the interior of your office + the interior of your refrigerator + the lumen of your gut + your left nostril (a fiat part – the opening – of your left nasal cavity) + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + site + + + + + b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) + + + + + + (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] + + + + + + + + + + object + Object + atom + cell + cells and organisms + engineered artifacts + grain of sand + molecule + organelle + organism + planet + solid portions of matter + star + BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. + BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). + BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 + BFO 2 Reference: an object is a maximal causally unified material entity + BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 + b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) + + object + + + + + b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + function + Function + the function of a hammer to drive in nails + the function of a heart pacemaker to regulate the beating of a heart through electricity + the function of amylase in saliva to break down starch into sugar + BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + function + + + + + A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) + + + + + + (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] + + + + + + + + + + p-boundary + ProcessBoundary + the boundary between the 2nd and 3rd year of your life. + p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) + Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) + (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] + (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] + + process boundary + + + + + p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) + + + + + + Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) + + + + + + (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] + + + + + + (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] + + + + + + + + + + + 1d-t-region + OneDimensionalTemporalRegion + the temporal region during which a process occurs. + BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). + A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) + (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] + + one-dimensional temporal region + + + + + A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) + + + + + + (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] + + + + + + + + + + + material + MaterialEntity + material entity + material entity + a flame + a forest fire + a human being + a hurricane + a photon + a puff of smoke + a sea wave + a tornado + an aggregate of human beings. + an energy wave + an epidemic + the undetached arm of a human being + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 + BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. + BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + material entity + material entity + + + + + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) + + + + + + Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) + + + + + + every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) + + + + + + (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] + + + + + + (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] + + + + + + + + + + cf-boundary + ContinuantFiatBoundary + b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) + BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. + BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 + Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. + Every continuant fiat boundary is located at some spatial region at every time at which it exists + (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] + + continuant fiat boundary + + + + + b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) + + + + + + Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. + + + + + + (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] + + + + + + + + + + immaterial + ImmaterialEntity + BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 + + immaterial entity + + + + + + + + + + + 1d-cf-boundary + OneDimensionalContinuantFiatBoundary + The Equator + all geopolitical boundaries + all lines of latitude and longitude + the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. + the median sulcus of your tongue + a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) + (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] + + one-dimensional continuant fiat boundary + + + + + a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) + + + + + + (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] + + + + + + + + + + + process-profile + ProcessProfile + On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels + One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. + The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. + b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) + b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) + (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] + (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] + + process profile + + + + + b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) + + + + + + b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) + + + + + + (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] + + + + + + (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] + + + + + + + + + + r-quality + RelationalQuality + John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. + a marriage bond, an instance of love, an obligation between one person and another. + a marriage bond, an instance of requited love, an obligation between one person and another. + b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) + (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] + + relational quality + + + + + b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) + + + + + + (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] + + + + + + + + + + 2d-cf-boundary + TwoDimensionalContinuantFiatBoundary + a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) + (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] + + two-dimensional continuant fiat boundary + + + + + a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) + + + + + + (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] + + + + + + + + + + 0d-cf-boundary + ZeroDimensionalContinuantFiatBoundary + the geographic North Pole + the point of origin of some spatial coordinate system. + the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet + zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. + a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) + (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] + + zero-dimensional continuant fiat boundary + + + + + zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. + + requested by Melanie Courtot + + + + + + a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) + + + + + + (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] + + + + + + + + + + 0d-t-region + ZeroDimensionalTemporalRegion + a temporal region that is occupied by a process boundary + right now + the moment at which a child is born + the moment at which a finger is detached in an industrial accident + the moment of death. + temporal instant. + A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) + (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] + + zero-dimensional temporal region + + + + + A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) + + + + + + (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] + + + + + + + + + + history + History + A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) + + history + + + + + A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) + + + + + + + + + + + insulin + A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. + + insulin + + + + + + + + + water + An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. + + water + + + + + + + + + ATP + An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. + + ATP + + + + + + + + + + + + + + + biotin + An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. + + biotin + + + + + + + + + cholesterol + A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. + + cholesterol + + + + + + + + + ammonia + An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. + + ammonia + + + + + + + + + phospholipid + A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. + + phospholipid + + + + + + + + + nitrite + The nitrogen oxoanion formed by loss of a proton from nitrous acid. + + nitrite + + + + + + + + + carbon dioxide + A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. + + carbon dioxide + + + + + + + + + peptide + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + + peptide + + + + + + + + + + globulin type + One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. + + globulin type + + + + + + + + + creatinine + A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. + + creatinine + + - - + + + + + mycophenolic acid + A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. + + mycophenolic acid + - + + + creatine + A glycine derivative having methyl and amidino groups attached to the nitrogen. + + creatine + - + + + bilirubin IXalpha + A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. + + bilirubin IXalpha + - + + + deoxyribonucleic acid + High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. + + deoxyribonucleic acid + - + + + progesterone + A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. + + progesterone + - + + + hydrogensulfite + + hydrogensulfite + - + + + + homocysteine + A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. + + homocysteine + - + + + glucose + An aldohexose used as a source of energy and metabolic intermediate. + + glucose + - + + + testosterone + An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. + + testosterone + - + + + + methemoglobin + A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. + + methemoglobin + - + + + hydrogencarbonate + The carbon oxoanion resulting from the removal of a proton from carbonic acid. + + hydrogencarbonate + - + + + cortisol + A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses + + cortisol + + + + + + + + + 5'-adenylyl sulfate + An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. + + 5'-adenylyl sulfate + - + + + triglyceride + Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. + + triglyceride + - + + + chloride + A halide anion formed when chlorine picks up an electron to form an an anion. + + chloride + - + + + + 3-hydroxybutyric acid + A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. + + 3-hydroxybutyric acid + - + + + bile salt + A sodium salt of the conjugate of any bile acid with either glycine or taurine. + + bile salt + + + molecular entity + Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well + + molecular entity - + + + cytochalasin + + cytochalasin + - + + + estradiol + A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. + + estradiol + - + + + N-ethyl-N-nitrosourea + A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. + + N-ethyl-N-nitrosourea + + + + + + + + + proton + Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + + proton + - + + + iron cation + + iron cation + + + + + + + + + luciferin + A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. + + luciferin + - + + + amikacin + An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. + + amikacin + - + + + sodium chloride + An inorganic chloride salt having sodium(1+) as the counterion. + + sodium chloride + - + + + uric acid + An oxopurine that is the final oxidation product of purine metabolism. + + uric acid + - + + + lead(0) + + lead(0) + - + + + + vancomycin + A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. + + vancomycin + - + + + rac-lactic acid + A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. + + rac-lactic acid + - + + + acrylamide + A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. + + acrylamide + - + + + dehydroepiandrosterone + An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. + + dehydroepiandrosterone + - + + + + 3,3',5'-triiodothyronine + + 3,3',5'-triiodothyronine + - + + + tobramycin + A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. + + tobramycin + - + + + sodium(1+) + A monoatomic monocation obtained from sodium. + + sodium(1+) + - + + + potassium(1+) + A monoatomic monocation obtained from potassium. + + potassium(1+) + - + + + hydroxyl + + hydroxyl + - + + + + deuterium atom + The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). + + deuterium atom + - + + + + thyroxine + An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. + + thyroxine + - + + + ruthenium atom + + ruthenium atom + + + fluorescein (lactone form) + A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy. + + fluorescein (lactone form) + + + + + + + + + gadodiamide hydrate + The hydrate of gadodiamide. + + gadodiamide hydrate + + + + + + + + + gadoteridol + A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). + + gadoteridol + + + + + + + + + phenol red + 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. + + phenol red - + + + sodium citrate dihydrate + The dihydrate of trisodium citrate. + + sodium citrate dihydrate + - + + + atom + A chemical entity constituting the smallest component of an element having the chemical properties of the element. + + atom + - + + + elemental oxygen + + elemental oxygen + - + + + rare earth metal atom + + rare earth metal atom + - + + + rhodium atom + A cobalt group element atom of atomic number 45. + + rhodium atom + + + + + + + + + gadolinium atom + + gadolinium atom + - + + + terbium atom + + terbium atom + - + + + nucleic acid + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + + nucleic acid + - + + + ribonucleic acid + High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. + + ribonucleic acid + - + + + amino acid + A carboxylic acid containing one or more amino groups. + + amino acid + + + macromolecule + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer + + macromolecule - + + + + hemoglobin + + hemoglobin + - + + + fatty acid + Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. + + fatty acid + + + + + + + + + gadolinium molecular entity + + gadolinium molecular entity + - + + + phosphate ion + A phosphorus oxoanion that is the conjugate base of phosphoric acid. + + phosphate ion + + + + + + + + + gadodiamide + A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). + + gadodiamide + - + + + folic acids + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + + folic acids + - + + + sodium phosphate + + sodium phosphate + + + phosphorus-32 atom + The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. + + phosphorus-32 atom @@ -2002,12 +5514,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + phosphorus-33 atom + The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. + + phosphorus-33 atom @@ -2015,12 +5532,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + Cy3 dye + + Cy3 dye @@ -2028,116 +5549,216 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + Cy5 dye + + Cy5 dye - + + + high-density lipoprotein + A class of lipoproteins of small size (4-13 nm) and dense (greater than 1.063 g/ml) particles. They are synthesized in the liver without a lipid core, accumulate cholesterol esters from peripheral tissues and transport them to the liver for re-utilization or elimination from the body (the reverse cholesterol transport). + + high-density lipoprotein + - + + + low-density lipoprotein + A class of lipoproteins of small size (18-25 nm) and low density (1.019-1.063 g/ml) particles with a core composed mainly of cholesterol esters and smaller amounts of triglycerides. The surface monolayer consists mostly of phospholipids, a single copy of apolipoprotein B-100, and free cholesterol molecules. The main function of LDL is to transport cholesterol and cholesterol esters from the liver. Excessive levels are associated with cardiovascular disease. + + low-density lipoprotein + - + + + very-low-density lipoprotein + A class of lipoproteins of large size (30-80 nm), very low density (0.93-1.006 g/ml) particles with a core composed mainly of triglycerides and a surface monolayer of phospholipids and cholesterol into which are imbedded the apolipoproteins B, E, and C. VLDL facilitate the transport of endogenously made triglycerides to extrahepatic tissues. + + very-low-density lipoprotein + - + + + + calcium cation + + calcium cation + - + + + calcium ion + + calcium ion + - + + + magnesium cation + Any magnesium ion that is positively charged. + + magnesium cation + - + + + valproic acid + A branched-chain saturated fatty acid that comprises of a propyl substituent on a pentanoic acid stem. + + valproic acid + + + digoxigenin + A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. + + digoxigenin + + + + + + + + + ethylenediaminetetraacetic acid + + ethylenediaminetetraacetic acid - + + + digoxin + A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. + + digoxin + - + + + double-stranded DNA + + double-stranded DNA + - + + + 5-bromo-2'-deoxyuridine + A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. + + 5-bromo-2'-deoxyuridine + - + + + low-density lipoprotein cholesterol + Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). + + low-density lipoprotein cholesterol + - + + + high-density lipoprotein cholesterol + Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). + + high-density lipoprotein cholesterol + - + + + chromium-51 + A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. + + chromium-51 + + + Alexa Fluor 532 + + Alexa Fluor 532 @@ -2145,12 +5766,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + Alexa Fluor 546 + + Alexa Fluor 546 @@ -2158,97 +5783,221 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + Alexa Fluor 555 + A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. + + Alexa Fluor 555 - + + + tritiated thymidine + Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. + + tritiated thymidine + - + + + dimethyl sulfate + The dimethyl ester of sulfuric acid. + + dimethyl sulfate + - + + + diethyl pyrocarbonate + The diethyl ester of dicarbonic acid. + + diethyl pyrocarbonate + - + + + 1,1-dihydroxy-3-ethoxy-2-butanone + A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. + + 1,1-dihydroxy-3-ethoxy-2-butanone + + + + + + + + + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide + A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. + + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide + - + + + N-methylisatoic anhydride + A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. + + N-methylisatoic anhydride + - + + + (S)-1-(4-bromoacetamidobenzyl)EDTA + A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. + + (S)-1-(4-bromoacetamidobenzyl)EDTA + - + + + EDTA methidiumpropylamide + A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. + + EDTA methidiumpropylamide + + + + + + + + + bromophenol blue + 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. + + bromophenol blue + - + + + tacrolimus hydrate + A hydrate that is the monohydrate form of tacrolimus. + + tacrolimus hydrate + - + + + oxygen radical + An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. + + oxygen radical + - + + + + lipoprotein + A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. + + lipoprotein + - + + + + thyroid stimulating hormone + + thyroid stimulating hormone + - + + + Luteinizing hormone + + Luteinizing hormone + - + + + Follicle stimulating hormone + + Follicle stimulating hormone + - + + + 25-hydroxyvitamin D2 + A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. + + 25-hydroxyvitamin D2 + + + + + + + + + tris + A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. + + tris + @@ -2272,12 +6021,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. - FM - fluorescence imaging - fluorescence microscopic imaging - CHMO - fluorescence microscopy assay + Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. + FM + fluorescence imaging + fluorescence microscopic imaging + CHMO + fluorescence microscopy assay @@ -2286,18 +6035,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. - CLSM - LSCM - confocal fluorescence imaging - confocal laser scanning fluorescence microscopy - confocal laser scanning microscopy - confocal-laser scanning microscopy - fluorescence confocal microscopy - fluorescence confocal scanning laser microscopy - scanning confocal fluorescence microscopy - CHMO - confocal fluorescence microscopy assay + Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. + CLSM + LSCM + confocal fluorescence imaging + confocal laser scanning fluorescence microscopy + confocal laser scanning microscopy + confocal-laser scanning microscopy + fluorescence confocal microscopy + fluorescence confocal scanning laser microscopy + scanning confocal fluorescence microscopy + CHMO + confocal fluorescence microscopy assay @@ -2306,12 +6055,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. - OM - light microscopy - optical microscopy - CHMO - light microscopy assay + Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. + OM + light microscopy + optical microscopy + CHMO + light microscopy assay @@ -2320,18 +6069,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. - LC-MS-MS - LC-MS/MS - LC-MS2 - LC-MSMS - LC/MS/MS - LCMSMS - liquid chromatography tandem mass spectrometry - liquid chromatography tandem mass spectroscopy - liquid chromatography-tandem mass spectroscopy + A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. + LC-MS-MS + LC-MS/MS + LC-MS2 + LC-MSMS + LC/MS/MS + LCMSMS + liquid chromatography tandem mass spectrometry + liquid chromatography tandem mass spectroscopy + liquid chromatography-tandem mass spectroscopy CHMO - liquid chromatography-tandem mass spectrometry + liquid chromatography-tandem mass spectrometry @@ -2339,6 +6088,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + @@ -2364,6 +6114,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + cell line cell + cell line cell + 细胞系细胞 + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture + + 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 + 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 + + + cell line cell + cell line cell + 细胞系细胞 @@ -2381,19 +6144,43 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + + mortal cell line cell + mortal cell line cell + 非永生细胞系细胞 + A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. + A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. + + mortal cell line cell + mortal cell line cell + 非永生细胞系细胞 + - + + + immortal cell line cell + immortal cell line cell + 永生细胞系细胞 + A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. + A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. + 预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。 + + immortal cell line cell + immortal cell line cell + 永生细胞系细胞 + + @@ -2406,6 +6193,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + cell line + 细胞系 + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). + + 一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 + 培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 + + + cell line + 细胞系 @@ -2413,6 +6211,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + @@ -2425,6 +6224,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + immortal cell line + A cell line that is expected to be capable of indefinite propagation in an vitro culture. + + immortal cell line @@ -2432,6 +6235,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + @@ -2451,6 +6255,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + mortal cell line + A cell line is able to support only a limited number of passages in vitro. + + mortal cell line @@ -2458,7 +6266,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + + cell @@ -2466,6 +6279,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + @@ -2496,15 +6310,32 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + primary cultured cell + A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. + + primary cultured cell - + - - - + + + native cell + A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + + native cell + + + + + + + + + + @@ -2522,623 +6353,1852 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + cultured cell + A cell in vitro that is or has been maintained or propagated as part of a cell culture. + + cultured cell + + + + + + + + + fibroblast + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. + + fibroblast + + + + + + + + + epithelial cell + A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. + + epithelial cell - + + + + mesothelial cell + A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + + mesothelial cell + - + + + T cell + A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. + + T cell + + + + + + + + + mast cell + A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. + + mast cell + + + + + + + + + hepatocyte + The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. + + hepatocyte + - + + + erythrocyte + A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. + + erythrocyte + - + + + + platelet + A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. + + platelet + - + + + macrophage + A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. + + macrophage + - + + + B cell + A lymphocyte of B lineage that is capable of B cell mediated immunity. + + B cell + + + + + + + + + dendritic cell + A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). + + dendritic cell + - + + + neuron + The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + + neuron + - + + + lymphocyte + A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. + + lymphocyte + - + + + megakaryocyte + A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm. + + megakaryocyte + - + + + reticulocyte + An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. + + reticulocyte + - + + + + + band form neutrophil + A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. + + band form neutrophil + - + + + + nucleate erythrocyte + An erythrocyte having a nucleus. + + nucleate erythrocyte + - + + + + + + monocyte + Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. + + monocyte + + + experimentally modified cell in vitro + A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. + + experimentally modified cell in vitro + + + + + + + + + CD4-positive, alpha-beta T cell + A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. + + CD4-positive, alpha-beta T cell + + + + + + + + + CD8-positive, alpha-beta T cell + A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. + + CD8-positive, alpha-beta T cell - + + + leukocyte + An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. + + leukocyte + - + + + basophil + Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. + + basophil + - + + + + + eosinophil + Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. + + eosinophil + - + + + + + neutrophil + Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. + + neutrophil + - + + + immature neutrophil + Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. + + immature neutrophil + - + + + plasma cell + A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. + + plasma cell + + + + + + + + + alpha-beta T cell + A T cell that expresses an alpha-beta T cell receptor complex. + + alpha-beta T cell + + + + + + + + + CD8-positive, alpha-beta cytotoxic T cell + A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. + + CD8-positive, alpha-beta cytotoxic T cell + + + + + + + + + mature NK T cell + A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. + + mature NK T cell + - + + + + promyelocyte + A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. + + promyelocyte + + + + + + + + + mononuclear cell + A leukocyte with a single non-segmented nucleus in the mature form. + + mononuclear cell + + + + + + + + + malignant cell + A neoplastic cell that is capable of entering a surrounding tissue + + malignant cell + - + + + + metamyelocyte + A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. + + metamyelocyte + - + + + + myelocyte + A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. + + myelocyte + - + + + neural cell + A cell that is part of the nervous system. + + neural cell + - + + + + + segmented neutrophil of bone marrow + A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. + + segmented neutrophil of bone marrow + + + + + + + + + + peripheral blood mononuclear cell + A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. + + peripheral blood mononuclear cell + - + + + complex of molecular entities + A complex of two or more molecular entities that are not covalently bound. + + complex of molecular entities + + + + + + + + + soil + Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms. + + soil + + + + + + + + + podzol + Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. + + podzol + - + + + environmental material + A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. + + environmental material + - + + + - + + + chromatin + The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + + chromatin + - + + + + core promoter sequence-specific DNA binding + Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. + + core promoter sequence-specific DNA binding + + + + + + + + + + - + + + + RNA-templated transcription + The synthesis of an RNA transcript from an RNA template. + + RNA-templated transcription + - + + + action potential + A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities. + + action potential + - + + + antibody-dependent cellular cytotoxicity + Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells. + + antibody-dependent cellular cytotoxicity + - + + + type IV hypersensitivity + An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation. + + type IV hypersensitivity + - + + + cytokine production + The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + cytokine production + - + + + cell killing + Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions. + + cell killing + - + + + T cell mediated cytotoxicity + The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. + + T cell mediated cytotoxicity + - + + + adaptive immune response + An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). + + adaptive immune response + + + + + + + + + cytokine production involved in immune response + The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. + + cytokine production involved in immune response + + + + + + + + + + - + + + tolerance induction + A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it. + + tolerance induction + - + + + B cell tolerance induction + A process involving any mechanism for tolerance induction in B cells. + + B cell tolerance induction + - + + + T cell tolerance induction + A process involving any mechanism for tolerance induction in T cells. + + T cell tolerance induction + - + + + hypersensitivity + An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system. + + hypersensitivity + + + + + + + + + cytokine production involved in inflammatory response + The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels. + + cytokine production involved in inflammatory response + - + + + glomerular filtration + The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein. + + glomerular filtration + - + + + molecular_function + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. + + molecular_function + + + + + + + + + antigen binding + Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. + + antigen binding + - + + + catalytic activity + Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. + + catalytic activity + + + + + + + + + L-iditol 2-dehydrogenase activity + Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+. + + L-iditol 2-dehydrogenase activity + - + + + RNA-directed DNA polymerase activity + Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. + + RNA-directed DNA polymerase activity + - + + + acetylcholinesterase activity + Catalysis of the reaction: acetylcholine + H2O = choline + acetate. + + acetylcholinesterase activity + + + + + + + + + acyl-CoA oxidase activity + Catalysis of the reaction: acyl-CoA + O2 = trans-2,3-dehydroacyl-CoA + hydrogen peroxide. + + acyl-CoA oxidase activity + + + + + + + + + L-alanine:2-oxoglutarate aminotransferase activity + Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate. + + L-alanine:2-oxoglutarate aminotransferase activity + + + + + + + + + alkaline phosphatase activity + Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum. + + alkaline phosphatase activity + + + + + + + + + L-aspartate:2-oxoglutarate aminotransferase activity + Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate. + + L-aspartate:2-oxoglutarate aminotransferase activity + + + + + + + + + cholinesterase activity + Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion. + + cholinesterase activity + + + + + + + + + creatine kinase activity + Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). + + creatine kinase activity + + + + + + + + + glutamate dehydrogenase [NAD(P)+] activity + Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+. + + glutamate dehydrogenase [NAD(P)+] activity + - + + + glutathione transferase activity + Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group. + + glutathione transferase activity + + + + + + + + + isocitrate dehydrogenase [NAD(P)+] activity + Catalysis of the reaction: isocitrate + NAD(P)+ = 2-oxoglutarate + CO2 + NAD(P)H. + + isocitrate dehydrogenase [NAD(P)+] activity + + + + + + + + + lactate dehydrogenase activity + Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate. + + lactate dehydrogenase activity + + + + + + + + + ribonuclease activity + Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. + + ribonuclease activity + - + + + ion channel activity + Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size). + + ion channel activity + - + + + cellular_component + A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). + + cellular_component + - + + + fibrinogen complex + A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds. + + fibrinogen complex + - + + + chromosome + A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. + + chromosome + + + + + + + + + mitochondrion + A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. + + mitochondrion + + + + + + + + + glucose metabolic process + The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides. + + glucose metabolic process + - + + + DNA replication + The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. + + DNA replication + - + + + DNA methylation + The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. + + DNA methylation + - + + + chromatin remodeling + A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication. + + chromatin remodeling + + + + + + + + + phagocytosis + A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. + + phagocytosis + - + + + immune response + Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. + + immune response + - + + + cellular response to DNA damage stimulus + Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism. + + cellular response to DNA damage stimulus + - + + + cell cycle + The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. + + cell cycle + - + + + blood coagulation + The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. + + blood coagulation + + + biological_process + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + + biological_process - + + + opsonization + The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody. + + opsonization + + + + + + + + + 5'-nucleotidase activity + Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate. + + 5'-nucleotidase activity + - + + + cell population proliferation + The multiplication or reproduction of cells, resulting in the expansion of a cell population. + + cell population proliferation + - + + + fertilization + The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy). + + fertilization + - + + + cellular process + Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + + cellular process + - + + + gene expression + The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes. + + gene expression + - + + + vascular endothelial growth factor production + The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + vascular endothelial growth factor production + + + + + + + + + galactosidase activity + Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative. + + galactosidase activity + - + + + immunoglobulin mediated immune response + An immune response mediated by immunoglobulins, whether cell-bound or in solution. + + immunoglobulin mediated immune response + + + + + + + + + amylase activity + Catalysis of the hydrolysis of amylose or an amylose derivative. + + amylase activity + + + + + + + + + beta-N-acetylglucosaminidase activity + Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides. + + beta-N-acetylglucosaminidase activity + - + + + histone modification + The covalent alteration of one or more amino acid residues within a histone protein. + + histone modification + - + + + hydrolase activity, acting on ester bonds + Catalysis of the hydrolysis of any ester bond. + + hydrolase activity, acting on ester bonds + - + + + immunoglobulin complex + A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + + immunoglobulin complex + - + + + B cell receptor complex + An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. + + B cell receptor complex + - + + + antigen processing and presentation + The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. + + antigen processing and presentation + - + + + protein domain specific binding + Binding to a specific domain of a protein. + + protein domain specific binding + - + + + actin filament polymerization + Assembly of actin filaments by the addition of actin monomers to a filament. + + actin filament polymerization + - + + + hemopoiesis + The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates. + + hemopoiesis + + + + + + + + + connective tissue growth factor production + The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + connective tissue growth factor production + + + + + + + + + chemokine production + The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria. + + chemokine production + - + + + granulocyte macrophage colony-stimulating factor production + The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + granulocyte macrophage colony-stimulating factor production + + + + + + + + + hepatocyte growth factor production + The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + hepatocyte growth factor production + + + + + + + + + type I interferon production + The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. + + type I interferon production + - + + + interferon-alpha production + The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interferon-alpha production + - + + + interferon-beta production + The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interferon-beta production + - + + + interferon-gamma production + The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. + + interferon-gamma production + - + + + interleukin-1 alpha production + The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-1 alpha production + - + + + interleukin-1 beta production + The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-1 beta production + + + + + + + + + interleukin-1 production + The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-1 production + - + + + interleukin-10 production + The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-10 production + + + + + + + + + interleukin-11 production + The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-11 production + - + + + interleukin-12 production + The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-12 production + - + + + interleukin-13 production + The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-13 production + + + + + + + + + obsolete interleukin-14 production + OBSOLETE. The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + obsolete interleukin-14 production + - + + + interleukin-15 production + The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-15 production + - + + + interleukin-16 production + The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-16 production + - + + + interleukin-17 production + The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-17 production + - + + + interleukin-18 production + The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-18 production + + + + + + + + + interleukin-19 production + The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-19 production + - + + + interleukin-2 production + The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-2 production + + + + + + + + + interleukin-20 production + The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-20 production + - + + + interleukin-21 production + The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-21 production + - + + + interleukin-22 production + The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-22 production + - + + + interleukin-23 production + The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-23 production + + + + + + + + + interleukin-24 production + The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-24 production + + + + + + + + + interleukin-25 production + The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-25 production + + + + + + + + + interleukin-26 production + The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-26 production + - + + + interleukin-27 production + The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-27 production + - + + + interleukin-3 production + The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-3 production + - + + + interleukin-4 production + The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-4 production + - + + + interleukin-5 production + The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-5 production + - + + + interleukin-6 production + The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-6 production + - + + + interleukin-7 production + The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-7 production + - + + + interleukin-8 production + The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-8 production + - + + + interleukin-9 production + The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-9 production + + + + + + + + + TRAIL production + The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + TRAIL production + - TNF alpha production + + tumor necrosis factor production + The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis. + TNF alpha production + + tumor necrosis factor production @@ -3146,7 +8206,48 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - TNF beta production + + lymphotoxin A production + The chemical reactions and pathways resulting in the formation of the cytokine lymphotoxin A. + TNF beta production + + lymphotoxin A production + + + + + + + + + transforming growth factor beta1 production + The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + transforming growth factor beta1 production + + + + + + + + + transforming growth factor beta2 production + The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + transforming growth factor beta2 production + + + + + + + + + transforming growth factor beta3 production + The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + transforming growth factor beta3 production @@ -3154,101 +8255,201 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + protein-containing complex A ribosome is a protein complex. + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. protein complex + + protein-containing complex - + + + macromolecule localization + Any process in which a macromolecule is transported to, or maintained in, a specific location. + + macromolecule localization + - + + + DNA polymerase activity + Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group. + + DNA polymerase activity + + + + + + + + + type III interferon production + The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far. + + type III interferon production + - + + + chemokine (C-X-C motif) ligand 9 production + The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-X-C motif) ligand 9 production + - + + + helper T cell enhancement of adaptive immune response + Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell. + + helper T cell enhancement of adaptive immune response + - + + + helper T cell enhancement of T cell mediated immune response + Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell. + + helper T cell enhancement of T cell mediated immune response + - + + + helper T cell enhancement of B cell mediated immune response + Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell. + + helper T cell enhancement of B cell mediated immune response + - + + + granzyme A production + The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + granzyme A production + - + + + perforin production + The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + perforin production + - + + + granulysin production + The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + granulysin production + - + + + chemokine (C-C motif) ligand 20 production + The appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-C motif) ligand 20 production + - + + + T cell proliferation + The expansion of a T cell population by cell division. Follows T cell activation. + + T cell proliferation + - + + + T cell receptor complex + A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. + + T cell receptor complex + - + + + T cell activation + The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. + + T cell activation + - antibody - antibody + + immunoglobulin complex, circulating + An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. + antibody + + antibody + immunoglobulin complex, circulating @@ -3256,6 +8457,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + @@ -3267,4504 +8469,5340 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + DNA polymerase complex + A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. + + DNA polymerase complex + + + + + + + + + peptide antigen binding + Binding to an antigen peptide. + + peptide antigen binding - + + + MHC protein complex + A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. + + MHC protein complex + + + + + + + + + membrane-bounded organelle + Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + + membrane-bounded organelle + - + + + cytotoxic T cell degranulation + The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell. + + cytotoxic T cell degranulation + - + + + sequence-specific DNA binding + Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. + + sequence-specific DNA binding + - + + + regulation of DNA methylation + Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. + + regulation of DNA methylation + - + + + macrophage migration inhibitory factor production + The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + macrophage migration inhibitory factor production + - + + + oncostatin M production + The appearance of oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + oncostatin M production + - + + + chemokine (C-C motif) ligand 17 production + The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-C motif) ligand 17 production + + + + + + + + + D-glutamyltransferase activity + Catalysis of the reaction: L(or D)-glutamine + D-glutamyl-peptide = NH3 + 5-glutamyl-D-glutamyl-peptide. + + D-glutamyltransferase activity + - + + + cellular developmental process + A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. + + cellular developmental process + - + + + response to stimulus + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. + + response to stimulus + - + + + chromosome organization + A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome. + + chromosome organization + - + + + carboxylic ester hydrolase activity + Catalysis of the hydrolysis of a carboxylic ester bond. + + carboxylic ester hydrolase activity + - + + + ferritin complex + A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain. + + ferritin complex + + + + + + + + + actin polymerization-dependent cell motility + A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell. + + actin polymerization-dependent cell motility + - + + + transforming growth factor beta production + The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3. + + transforming growth factor beta production + - + + + monocyte chemotactic protein-1 production + The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + monocyte chemotactic protein-1 production + - + + + chemokine (C-C motif) ligand 4 production + The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-C motif) ligand 4 production + - + + + macrophage inflammatory protein-1 gamma production + The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + macrophage inflammatory protein-1 gamma production + - + + + macrophage inflammatory protein-1 alpha production + The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + macrophage inflammatory protein-1 alpha production + - + + + chemokine (C-C motif) ligand 5 production + The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-C motif) ligand 5 production + - + + + chemokine (C-C motif) ligand 1 production + The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-C motif) ligand 1 production + - + + + granulocyte colony-stimulating factor production + The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + granulocyte colony-stimulating factor production + - + + + IP-10 production + The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + IP-10 production + - + + + granzyme B production + The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + granzyme B production + - + + + tumor necrosis factor superfamily cytokine production + The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + tumor necrosis factor superfamily cytokine production + - + + + IgG immunoglobulin complex + A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + + IgG immunoglobulin complex + - + + + IgE immunoglobulin complex + A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + + IgE immunoglobulin complex + - + + + IgA immunoglobulin complex + A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + + IgA immunoglobulin complex + - + + + IgM immunoglobulin complex + A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. + + IgM immunoglobulin complex + - + + + chemokine (C-C motif) ligand 22 production + The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-C motif) ligand 22 production + - + + + tumor necrosis factor (ligand) superfamily member 11 production + The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + tumor necrosis factor (ligand) superfamily member 11 production + - + + + interleukin-17A production + The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-17A production + - + + + interleukin-17F production + The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + interleukin-17F production + - + + + complement-dependent cytotoxicity + Cell killing caused by the membrane attack complex formed following complement activation. + + complement-dependent cytotoxicity + - + + + histamine secretion mediated by immunoglobulin + Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface. + + histamine secretion mediated by immunoglobulin + - + + + immune complex formation + The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus. + + immune complex formation + - + + + immunoglobulin-mediated neutralization + The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. + + immunoglobulin-mediated neutralization + - + + + chemokine (C-C motif) ligand 19 production + The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-C motif) ligand 19 production + - + + + chemokine (C-C motif) ligand 21 production + The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-C motif) ligand 21 production + - + + + chemokine (C-X-C motif) ligand 12 production + The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-X-C motif) ligand 12 production + - + + + chemokine (C-X-C motif) ligand 13 production + The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-X-C motif) ligand 13 production + - + + + chemokine (C-X-C motif) ligand 16 production + The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + chemokine (C-X-C motif) ligand 16 production + - + + + amphiregulin production + The appearance of amphiregulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Amphiregulin (AREG) is a ligand of the epidermal growth factor receptor (EGFR), a widely expressed transmembrane tyrosine kinase. AREG is synthesized as a membrane-anchored precursor protein that can engage in juxtacrine signaling on adjacent cells. Alternatively, after proteolytic processing by cell membrane proteases, mainly TACE/ADAM17, AREG is secreted and behaves as an autocrine or paracrine factor. + + amphiregulin production + - + - + + + XCL1 production + The appearance of XCL1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. + + XCL1 production + + + + + + + + + Insulin resistance + Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels. + + Insulin resistance + - + + + conditional specification + + A directive information entity that specifies what should happen if the trigger condition is fulfilled. + PlanAndPlannedProcess Branch + OBI branch derived + OBI_0000349 + conditional specification + - + + + measurement unit label + Examples of measurement unit labels are liters, inches, weight per volume. + + A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. + 2009-03-16: provenance: a term measurement unit was +proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and +Cristian Cocos, and subsequently moved to IAO where the objective for +which the original term was defined was satisfied with the definition +of this, different, term. + 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + measurement unit label + - + + + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + + A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + objective specification + - + + + narrative object + Examples of narrative objects are reports, journal articles, and patents submission. + + A narrative object is an information content entity that is a set of propositions. + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion + agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions + person:Chris Stoeckert + OBI_0000013 + group:OBI + narrative object + - + - + + + Pour the contents of flask 1 into flask 2 + + A directive information entity that describes an action the bearer will take. + Alan Ruttenberg + OBI Plan and Planned Process branch + action specification + - + - + + + + obsolete_artifact + true + - + - + + + datum label + + A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label + http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n + GROUP: IAO + 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. + + datum label + - + - + + + software + + Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit. + see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert + PERSON: Melanie Courtot + GROUP: OBI + software + - - - - - + - + + + obsolete_digital entity + A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. + 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - - - - - - - +Superclass was 'digitial quality' + person:Chris Stoeckert + OBI_0000261 + group:OBI + + obsolete2_digital entity + true - + - + + + journal article + Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. + + A report that is published in a journal. + person:Alan Ruttenberg + person:Chris Stoeckert + OBI_0000159 + group:OBI + journal article + - + - + + + + + + + + + + + + + + information carrier + In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. + + A quality of an information bearer that imparts the information content + 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. + 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. + PERSON: Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + information carrier + - + - + + + model number + + A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. + manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers + Person: Alan Ruttenberg + model number + - + - + + + + obsolete_material_entity + true + - + - + + + binary digital entity + MS Word document, ZIP file, DICOM file, JPEG file + A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. + 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 +Superclass was 'digital entity' + digital_entity + person:Chris Stoeckert + OBI_0000244 + group:OBI + + obsolete2_binary digital entity + true + - + - + + + The length of a ruler. + a unit of measure is the quality of some material entity compared to which another quality is some multiple of. + Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + obsolete_unit of measure + true + - + - + + + programming language + R, Perl, Java + + A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. + person:Alan Ruttenberg + person:Chris Stoeckert + OBI_0000058 + group:OBI + programming language + - + - + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item + - + - + + + symbol + a serial number such as "12324X" + a stop sign + a written proper name such as "OBI" + + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 20091104, MC: this needs work and will most probably change + 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). + PERSON: James A. Overton + PERSON: Jonathan Rees + based on Oxford English Dictionary + symbol + - + - + + + numeral + + A symbol that denotes a number. + PERSON: Jonathan Rees + numeral + - + - + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + - + - + + + integer numeral + + A numeral that denotes an integer + PERSON: Jonathan Rees + integer numeral + - + - + + - + - - - - - - - - - + + 1 - - + + 1 + 10 feet. 3 ml. + + A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. + 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in +this case we explicitly refer to the singular form + Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + scalar measurement datum - + - + + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO + Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + directive information entity + - + - + + + time trigger + + PlanAndPlannedProcess Branch + time trigger + - + - + + + obsolete_study interpretation + + A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses + 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. + Lawrence Hunter + PERSON: Alan Ruttenberg + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + conclusion + OBI_0000005 + + obsolete_study interpretation + true + - + - + + + dot plot + Dot plot of SSC-H and FSC-H. + + A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000123 + group:OBI + dot plot + - + - + + + graph + + A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. + PERSON: Lawrence Hunter + person:Alan Ruttenberg + person:Allyson Lister + OBI_0000240 + group:OBI + graph + - + - + + + text based digital entity + XML file, C++ source code file + A text based digital entity is a digital entity that is encoded so that it only contains text characters. + 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 +superclass was 'digital document' + digital_entity + person:Chris Stoeckert + OBI_0000132 + group:OBI + + obsolete2_text based digital entity + true + - + - + + + rule + example to be added + + A rule is an executable which guides, defines, restricts actions. + MSI + PRS + OBI_0500021 + PRS + rule + - + - + + + contour plot + Contour plot of SSC-H, FSC-H, and FL1-H. + + generically_dependent_continuants + person:Allyson Lister + person:Chris Stoeckert + OBI_0000246 + group:Flow Cytometry community + contour plot + - + - + + + report figure + + A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements + I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report + Replaced by defined version of figure + person:Alan Ruttenberg + person:Allyson Lister + OBI_0000027 + group:OBI + + obsolete2_report figure + true + - + - + + + algorithm + PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. + + A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. + Philippe Rocca-Serra + PlanAndPlannedProcess Branch + OBI_0000270 + adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + algorithm + - + - + + + software interpreter + R program, Perl interpreter, Java virtual machine + + A software interpreter is a software application that executes some specified input software. + Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter + person:Alan Ruttenberg + person:Chris Stoeckert + OBI_0000199 + group:OBI + software interpreter + - + - + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + - + - + + + density plot + Density plot of SSC-H and FSC-H. + + A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000179 + group:Flow Cytometry community + density plot + - + - + + + report + Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. + + A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). + 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on +something that has completed." Should it be restricted to those things +that are completed? For example, a progress report is (usually) about +something that definitely has *not* been completed, or may include +(only) projections. I think the definition would not suffer if the +whole sentence is deleted. + 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion + disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + PERSON:Chris Stoeckert + GROUP: OBI + OBI_0000099 + report + - + - + + + report element + + A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). + 2009-03-16: needs some more work (clarify relations). + 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion + Replaced by textual entity and figure + There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text + PERSON: Alan Ruttenberg + PERSON: Allyson Lister + PERSON: Melanie Courtot + GROUP:OBI + OBI_0000001 + + obsolete_report element + true + - + - + + + binary executable + Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) + 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 +superclass was 'digital entity' + person:Jennifer Fostel + OBI_0000222 + group:OBI + + obsolete2_binary executable + true + - + - + + + source code module + The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. + + A source code module is a directive information entity that specifies, using a programming language, some algorithm. + person:Alan Ruttenberg + person:Chris Stoeckert + OBI_0000039 + group:OBI + source code module + - + - + + + report table + + A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion + person:Alan Ruttenberg + person:Allyson Lister + OBI_0000265 + group:OBI + + obsolete_report table + true + - + - + + + data format specification + + A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file + 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file" + PERSON: Alan Ruttenberg + PlanAndPlannedProcess Branch + OBI branch derived + OBI_0000187 + data format specification + - + - + + + data set + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000042 + group:OBI + data set + - + - + + + image + + An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. + person:Alan Ruttenberg + person:Allyson + person:Chris Stoeckert + OBI_0000030 + group:OBI + image + - + - + + + data about an ontology part + Data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + - - - - + + + + + + + + + + + + + + + + plan specification + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. + + A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2014-03-31: A plan specification can have other parts, such as conditional specifications. + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + Alan Ruttenberg + OBI Plan and Planned Process branch + OBI_0000344 + 2/3/2009 Comment from OBI review. - +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. - +Request that IAO either clarify these or change definitions not to use them + plan specification + - + - + + + digital document + A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. + 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 +superclass was 'digial entity' + person:Jennifer Fostel + OBI_0000195 + group:OBI + + obsolete2_digital document + true + - + - + + + + + + + + + measurement datum + Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + measurement datum + - + + + + + + _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - +Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. + + obsolete_identifier + true + - + - + + + version number + + A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. + Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version + GROUP: IAO + version number + - + - + + + serial number + + A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. + Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) + GROUP: IAO + serial number + - + - + + + lot number + + A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. + GROUP: IAO + batch number + lot number + - - - - + + + + + A settings datum is a datum that denotes some configuration of an instrument. + 2/3/2009 Feedback from OBI - +This should be a "setting specification". There is a question of whether it is information about a realizable or not. - +Pro other specification are about realizables. +Cons sometimes specifies a quality which is not a realizable. + Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. + setting datum + - + - + + + 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 + Need to rework digital entity. Digital quality was suggested by Barry. + + obsolete_digital quality + true + - + - + + + + + + + + + + + + + + + conclusion textual entity + that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 + + A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + 2009/10/23 Alan Ruttenberg: We need to work on the definition still + Person:Alan Ruttenberg + conclusion textual entity + - + - + + + + + + + + + + + + + + + + + + + material information bearer + A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. + a brain + a hard drive + + A material entity in which a concretization of an information content entity inheres. + GROUP: IAO + material information bearer + - + - + + + histogram + + A histogram is a report graph which is a statistical description of a +distribution in terms of occurrence frequencies of different event classes. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + GROUP:OBI + histogram + - + - + + + heatmap + + A heatmap is a report graph which is a graphical representation of data +where the values taken by a variable(s) are shown as colors in a +two-dimensional map. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + GROUP:OBI + heatmap + - + - + + + Venn diagram + + A Venn diagram is a report graph showing all hypothetically possible +logical relations between a finite collection of sets. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Venn_diagram + Venn diagram + - + - - human being + + + obsolete_survival curve + + A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + WEB: http://www.graphpad.com/www/book/survive.htm + + obsolete_survival curve + true - + - + + + dendrogram + Dendrograms are often used in computational biology to +illustrate the clustering of genes. + + A dendrogram is a report graph which is a tree diagram +frequently used to illustrate the arrangement of the clusters produced by a +clustering algorithm. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Dendrogram + dendrogram + - + - - - role of being consumer safety officer - Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm - Person charged with serving as CSO, FDA official who coordinates the review - - the role of a human being that is realized by enforcing regulations to ensure consumer safety - Jennifer Fostel - Person:Helen Parkinson - OBI, CDISC - role of being consumer safety officer + + + scatter plot + Comparison of gene expression values in two samples can be displayed in a scatter plot + + A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + scattergraph + WEB: http://en.wikipedia.org/wiki/Scatterplot + scatter plot - + - - - fluorescent reporter intensity - - A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. - person:Chris Stoeckert - group:OBI - From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem. - fluorescent reporter intensity + + + + A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. + PERSON:Alan Ruttenberg + PERSON:Joanne Luciano + PERSON:Melanie Courtot + WEB: http://en.wiktionary.org/wiki/photograph + photograph - + - + - - - + + + - - + + + + + + + - - + + - planned process - Injecting mice with a vaccine in order to test its efficacy - - A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process + + photographic print + + A photographic print is a material entity upon which a photograph generically depends. + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + photographic print - + - - - regulator role - Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 - - a regulatory role involved with making and/or enforcing relevant legislation and governmental orders - Person:Jennifer Fostel - regulator - OBI - regulator role + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification - + - - - biological feature identification objective + + + textual entity + Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. - Jennifer Fostel - biological feature identification objective + A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. + AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. + MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. + PERSON: Lawrence Hunter + text + textual entity - + - - - regulation-assigned role - Approval letter - - Regulation-assigned role is a regulatory role defined by legislation or governmental orders - Person: Jennifer Fostel - regulation-assigned role + + + + + + + + + citation + Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. + + A textual entity intended to identify a particular publication. + PERSON: Lawrence Hunter + citation - + - - - regulatory role - Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 - - a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. - GROUP: Role branch - OBI, CDISC - govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent - regulatory role + + + author identification + L. Hunter + + A textual entity intended to identify a particular author + PERSON: Lawrence Hunter + author identification - + - - - material supplier role - Jackson Labs is an organization which provide mice as experimental material - - a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. - Supplier role is a special kind of service, e.g. biobank - PERSON:Jennifer Fostel - material provider role - supplier - material supplier role + + + institutional identification + University of Colorado Denver School of Medicine + + A textual entity intended to identify a particular institution + PERSON: Lawrence Hunter + institutional identification - + - - - contract research organization role - - a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution - Person: Jennifer Fostel - contract research organization - contract research organization role + + + + + + + + + caption + Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. + + A textual entity that describes a figure + PERSON: Lawrence Hunter + caption - + - - - list-mode data file - An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used. + + + document title + Textual characteristics of traditional and Open Access scientific journals are similar - A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter. - One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people. - person:Chris Stoeckert - group:Flow Cytometry community - list-mode data file + A textual entity that names a document + PERSON: Lawrence Hunter + document title - + - - - - - - - - - classified data set + + + table + | T F +--+----- +T | T F +F | F F - A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. - PERSON: James Malone - PERSON: Monnie McGee - data set with assigned class labels - classified data set + A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions + PERSON: Lawrence Hunter + table - + - - + + + table of abbreviations + IAO information artifact ontology +OBI ontology of biomedical investiations +GO gene ontology + + A table where the constituent texts are abbreviations and their expansions + PERSON: Lawrence Hunter + table of abbreviations + + + + + + + + + figure + Any picture, diagram or table + + An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. + PERSON: Lawrence Hunter + figure + + + + + + + + + diagram + A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. + + A figure that expresses one or more propositions + PERSON: Lawrence Hunter + diagram + + + + + + + + + document + A journal article, patent application, laboratory notebook, or a book + + A collection of information content entities intended to be understood together as a whole + PERSON: Lawrence Hunter + document + + + + + + + + + publication + A journal article or book + + A document that has been accepted by a publisher + PERSON: Lawrence Hunter + publication + + + + + + + + - - + + - reference substance role - Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html + publication about an investigation + Most scientific journal articles - a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. - Person:Jennifer Fostel - reference substance - OBI - reference substance role + A publication that is about an investigation + PERSON: Lawrence Hunter + scientific publication + publication about an investigation - + - - - cytological stain role - haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin + + + patent + US Patent 6,449,603 - A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization - Person:Helen Parkinson - Person:Jennifer Fostel - cytological stain - cytological stain role + A document that has been accepted by a patent authority + PERSON: Lawrence Hunter + patent - + - - + + - - + + + document part + An abstract, introduction, method or results section. + + An information content entity that is part of a document. + PERSON: Lawrence Hunter + document part + + + + + + + + - - + + - centrifuge pellet role - Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet - - pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.. - GROUP: Role branch - OBI - 9Mar09 after discussion with process branch changed definition to include use of centrifuge; - centrifuge pellet role + abstract + The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. + + A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. + PERSON: Lawrence Hunter + abstract - + - - - clinical research coordinator role - - a worker role comprised of handling the administrative duties of a trial or study. - Person:Jennifer Fostel - clinical research coordinator - clinical research coordinator role + + + + + + + + + introduction to a publication about an investigation + Section labelled 'introduction' of a typical scientific journal article + + A part of a publication about an investigation that is about the objective specification (why the investigation is being done) + PERSON: Lawrence Hunter + background + introduction + introduction to a publication about an investigation - + - - + + - - + + + methods section + The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. + + A part of a publication about an investigation that is about the study design of the investigation + PERSON: Lawrence Hunter + experimental + experimental procedures + experimental section + methods + methods section + + + + + + + + - - + + - supernatant role - Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia + results section + The section labelled 'results' in a typical scientific journal article - supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material. - GROUP: Role branch - OBI - supernatant role + A part of a publication about an investigation that is about a study design execution + PERSON: Lawrence Hunter + results + results section - + - - + + + discussion section of a publication about an investigation + + A part of a publication about an investigation that is about the study interpretation of the investigation + PERSON: Lawrence Hunter + discussion + discussion section + discussion section of a publication about an investigation + + + + + + + + - + + references section + The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" + + A part of a document that has citations as parts + PERSON: Lawrence Hunter + references section + + + + + + + + - - - - - - - - - - - - + + - chromatography column - - Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. - Frank Gibson - http://en.wikipedia.org/wiki/Column_chromatography - open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 - chromatography column + author list + Lawrence Hunter and Kevin Brettonel Cohen + + A part of a document that enumerates the authors of the document + PERSON: Lawrence Hunter + author list - + - - + + - - + + - drug role - http://www.answers.com/topic/drug - 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. - 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act. + institution list + The University of Colorado Denver School of Medicine and the University of Colorado Boulder. - a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism - Role Branch - drug - OBI, CDISC - drug role + A part of a document that has parts that are institution identifications associated with the authors of the document + PERSON: Lawrence Hunter + institution list - + - - + + + author contributions section + LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. + + A part of a publication that is about the specific contributions of each author + PERSON: Lawrence Hunter + author contributions + contributions by the authors + author contributions section + + + + + + + + + acknowledgements section + The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript + + Part of a publication that is about the contributions of people or institutions other than the authors. + PERSON: Lawrence Hunter + acknowledgements + acknowledgments + acknowledgements section + + + + + + + + - - + + - pump valve switch - - A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. - FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument - OBI Instrument branch - OBI - pump valve switch + footnote + The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. + + A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. + PERSON: Lawrence Hunter + endnote + footnote - + - - - xenotransplantation + + + supplementary material to a document + + A part of a document that is segregated from the rest of the document due to its size + PERSON: Lawrence Hunter + additional information + appendix + supplemental information + supplementary material + supporting information + supplementary material to a document + + + + + + + + + table of contents - is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans - PlanAndPlannedProcess Branch - OBI branch derived - xenotransplantation + A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). + PERSON: Lawrence Hunter + table of contents - + - - - physical document - a book is a physical document - - A physical document is an object serving as a record of information by means of symbolic marks. - PERSON: Bjoern Peters - GROUP: OBI - physical document + + + table of figures + + A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). + PERSON: Lawrence Hunter + table of figures - + - - - waiting + + + running title - not actively doing anything to a material for a duration of time. - PERSON:Alan Ruttenberg - OBI branch derived - BP: I have doubts about the utility of this. - We need a better handling/modeling of time (January 2008) - waiting + A shorter version of a document title + PERSON: Lawrence Hunter + running title - + - - - - - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material + + + copyright section + This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. + + A document part that describes legal restrictions on making or distributing copies of the document + PERSON: Lawrence Hunter + copyright section - + - - + + - - + + - - + + 1 + + A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude + 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + Alan Ruttenberg + AR notes: We need to discuss whether it should include site. + cartesian spatial coordinate datum + http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + + + + + + + + - - + + + + + + + + + + + + - - + + 1 - chromatography device - - A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. - Frank Gibson - chromatography instrument - http://en.wikipedia.org/wiki/Chromatography - open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 - chromatography device + + A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region + Alan Ruttenberg + one dimensional cartesian spatial coordinate datum - + - - - - - - - - + + - - + + + + + + + + + + + + - - + + 1 - - + + 1 - mass spectrometer - LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific - - A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum - Frank Gibson - http://en.wikipedia.org/wiki/Mass_spectrometry - mass spectrometer - - - - - - - - - A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. - OBI Instrument branch - OBI Instrument branch - - obsolete_platform - true + A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region + Alan Ruttenberg + two dimensional cartesian spatial coordinate datum - + - - + + - - + + + + + + + + + + + + - - + + 1 - - + + 1 - - + + 1 - liquid chromatography mass spectrometry platform - A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. - OBI instrument branch - OBI Instrument branch - liquid chromatography mass spectrometry platform + A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region + Alan Ruttenberg + three dimensional cartesian spatial coordinate datum - + - - + + - - + + - - + + - microarray platform - A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. - OBI Instrument branch - OBI Instrument branch - microarray platform + A scalar measurement datum that is the result of measurement of length quality + Alan Ruttenberg + length measurement datum - + - - - ratio of collected to emitted light - 10% - - A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role - person:Chris Stoeckert - person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt - ratio of collected to emitted light + + + + + + + + + + + + denotator type + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type - + - - - software optimization objective + + + + + + + + + + + + + + + + - Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. - Jennifer Fostel - software optimization objective + A scalar measurement datum that is the result of measurement of mass quality + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Person:Alan Ruttenberg + mass measurement datum - + - - - notified body role - The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf + + + hypothesis textual entity + that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive - Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB. - Person: Jennifer Fostel - notified body - OBI, CDISC - notified body role + A textual entity that expresses an assertion that is intended to be tested. + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Person:Alan Ruttenberg + hypothesis textual entity - + - - - allotransplantation - - is the transplantation of organs between members of the same species. - PlanAndPlannedProcess Branch - OBI branch derived - allotransplantation + + + + + + + + + + + + + + + + + + A scalar measurement datum that is the result of measuring a temporal interval + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Person:Alan Ruttenberg + time measurement datum - + - - + + - - + + - gamma counter - A Geiger counter - - A processed material which measures gamma radiation - Frank Gibson - http://en.wikipedia.org/wiki/Gamma_counter - gamma counter + + A textual entity that is used as directive to deliver something to a person, or organization + 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 + postal address - + - - - trial monitor role + + + email address - a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study - Person:Jennifer Fostel - trial monitor - CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study. - trial monitor role + Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 + Person:Alan Ruttenberg + Person:Chris Stoeckart + email address - + - - - - - - - - - positive reference substance role - MMS mutagen - - a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response - Person: Jennifer Fostel - positive reference substance - positive reference substance role + + + author role + + A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + author role - + - - - polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether - PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. - - triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties - Philippe Rocca-Serra - adapted from Wikipedia before possible import from CHEBI - polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether + + + + + + + + + + + + + + + + A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing + Person:Alan Ruttenberg + data item extraction from journal article - + - + + - - + + - - + + + Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. + + A planned process in which a document is created or added to by including the specified input in it. + 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape + Bjoern Peters + wikipedia http://en.wikipedia.org/wiki/Documenting + documenting + + + + + + + + + line graph + + A line graph is a type of graph created by connecting a series of data +points together with a line. + PERSON:Chris Stoeckert + PERSON:Melanie Courtot + line chart + GROUP:OBI + WEB: http://en.wikipedia.org/wiki/Line_chart + line graph + + + + + + + + - - + + - - - - - - - - - - - - + + - investigation - Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation - - a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). - Bjoern Peters - OBI branch derived - Could add specific objective specification - Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core -editor = PRS - study - investigation + A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. + + A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity + 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. + Person:Alan Ruttenberg + Person:Bjoern Peters + Person:Melanie Courtot + assigning a CRID + assigning a centrally registered identifier - + - - + + - - + + - - + + - evaluant role - When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. - - a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role - Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) - examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") - GROUP: Role Branch - OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - evaluant role + + + + + + + Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. + + A planned process in which a CRID registry associates an information content entity with a CRID symbol + PERSON:Alan Ruttenberg + associating information with a CRID in the CRID registry + associating information with a centrally registered identifier in its registry - + - - - reporting party role - Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. - The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm - - a study personnel role played by a party who reports the outcome of a study component - MO:submitter mapped to this term. So, alternative term 'submitter' was added. - Jennifer Fostel - reporting party - submitter - OBI - reporting party role + + + a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. + MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. + + obsolete_establishing a CRID registry + true - + - - - - - - - - + + - - + + + The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. + + A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID symbol + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier symbol + + + + + + + + - - - - - - - - - - - - + + - + - - - - - - - - - - - - - - - - - - - + + + + - - - - assay - Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. - - A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. - 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. - PlanAndPlannedProcess Branch - measuring - scientific observation - OBI branch derived - study assay - any method - assay + The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. + + An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. + 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). + Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. + + Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier - + - - - quantitative confidence value - - A data item which is used to indicate the degree of uncertainty about a measurement. - person:Chris Stoeckert - group:OBI - quantitative confidence value + + + PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. + + A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + CRID registry + Original proposal from Bjoern, discussions at IAO calls + centrally registered identifier registry - + - - + + - - + + - sample preparation for assay - - A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. - PlanAndPlannedProcess Branch - study - OBI branch derived - sample preparation for assay + + + + + + + + + + + + + Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. + + A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol + PERSON: Alan Ruttenberg + PERSON: Bill Hogan + PERSON: Bjoern Peters + PERSON: Melanie Courtot + looking up a CRID + looking up a centrally registered identifier - + - - - diagnosis textual entity + + + + + + + + + + + + + + + + - diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. - Jennifer Fostel - diagnosis textual entity + time stamped measurement datum - + - - - unplanned occurrence effecting an investigation - Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used + + + + + + + + + pmid:20604925 - time-lapse live cell microscopy - a process which is external in origin to the investigation that has an impact on the outcome. - PERSON: Bjoern Peters - OBI - unplanned occurrence effecting an investigation + A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. + Alan Ruttenberg + experimental time series + time sampled measurement data set - + - - - eMedical record + + + written name + "Bill Clinton" + "The Eiffel Tower" + "United States of America" - An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. - person:Jennifer Fostel - article-without-pmid-or-doi:CDISCglossary - eMedical record - - - - - - - - - culture medium - A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 - - a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. - changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 -Modification made by JZ. - Person: Jennifer Fostel, Jie Zheng - OBI - culture medium + A textual entity that denotes a particular in reality. + PERSON: Bill Hogan + https://github.com/information-artifact-ontology/IAO/issues/114 + The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. + written name - + - - - electronic case report tabulation - - An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators. - person:Jennifer Fostel - CDISC glossary - electronic case report tabulation + + + + A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + software method - + - - - polystyrene tube - Polystyrene tubes can be used to contain tissue culture cells during centrifgation - - A polystyrene tube is a test tube made of polystyrene - PERSON: Chris Stoeckert - PERSON: Chris Stoeckert - polystyrene tube + + + + A software module is software composed of a collection of software methods. + PERSON: Melanei Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + software module - - - - - reagent role - Buffer, dye, a catalyst, a solvating agent. - - A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. - PERSON:Matthew Brush - reagent - PERSON:Matthew Brush - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - -May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. - - (copied from ReO) -Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. - -Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. + -In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). - reagent role + + + + A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + software library - + - - - role of regulator of chemical manufacturer - EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm - - a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture - Person: Jennifer Fostel - regulator of chemical manufacture - OBI - role of regulator of chemical manufacturer + + + + A software application is software that can be directly executed by some processing unit. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + software application - + - - - detector reagent role + + - a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. - 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances - One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009 - detector reagent role + A software script is software whose instructions can be executed using a software interpreter. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + software script - + - - - role of certified IRB professional - CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional - - a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA - Person:Helen Parkinson - Person:Jennifer Fostel - certified IRB professional - WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional - role of certified IRB professional + + + abbreviation textual entity + From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): + +BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. + A textual entity listing abbreviations and their expansions that are used in a document. + PERSON: Bill Baumgartner + + abbreviation textual entity - + - - + + - - + + - patient role - a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 - - a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider - GROUP:Role Branch - patient - OBI, CDISC - CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably - patient role + abbreviations section + The section labelled 'abbreviations' in a typical scientific journal article. + A part of a document where abbreviations and their long-forms used within the document are listed. + PERSON: Bill Baumgartner + abbreviations + abbreviations list + abbreviations used + list of abbreviations + list of abbreviations used + + abbreviations section - + - - - - - - - - + + - - + + + author information section + The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) + A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. + PERSON: Bill Baumgartner + author information + authors’ information + + author information section + + + + + + + + + author information textual entity + From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): + +IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. + A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. + PERSON: Bill Baumgartner + + author information textual entity + + + + + + + + - - + + - - material processing - A cell lysis, production of a cloning vector, creating a buffer. - - A planned process which results in physical changes in a specified input material - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca Serra - material transformation - OBI branch derived - material processing + author summary section + The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) + A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. + PERSON: Bill Baumgartner + author summary + summary + synopsis + Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) + + author summary section - + - - - protocol testing objective - - Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. - Jennifer Fostel - protocol testing objective + + + author summary textual entity + From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): + + +The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. + A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). + PERSON: Bill Baumgartner + Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). + + author summary textual entity - + - - + + - - + + - study subject role - Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. -Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. -Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. - - A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. - A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. - GROUP: Role Branch - OBI - Following OBI call November 2012,26th: - -1. it was decided there was no need for moving the children class and making them siblings of study subject role. -2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study - -This note closes the issue and validates the class definition to be part of the OBI core -editor = PRS - - participant under investigation role + availability section + The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). + A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. + PERSON: Bill Baumgartner + availability + + availability section - + - - - Rat 1A; first enrolled patient to receive treatment - - First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study - Role Branch - OBI - - obsolete_role of being first subject treated - true + + + availability textual entity + From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): + +Project home page:http://krux.googlecode.com + A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. + PERSON: Bill Baumgartner + + availability textual entity - + - - - measured expression level - Examples are quantified data from an expression microarray experiment, PCR measurements, etc. - - A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. - person:Chris Stoeckert - OBI Data Transformation branch - measured expression level + + + + + + + + + case report section + The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) + A part of a document about the medical history of a specific patient as it relates to the topic of the document. + PERSON: Bill Baumgartner + case presentation + case report + + case report section - + - - - responsible party role - he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm - - a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study - Person: Jennifer Fostel - responsible party - OBI - responsible party role + + + case report textual entity + Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): + +The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. + A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. + PERSON: Bill Baumgartner + + case report textual entity - + - - - principal investigator role - - a responsible party role played by a person responsible for the overall conduct of a study - Person: Jennifer Fostel - principal investigator - CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC) - principal investigator role + + + + + + + + + conclusion section + The section labelled 'conclusion' in a typical scientific journal article. + A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. + PERSON: Bill Baumgartner + concluding remarks + conclusion + conclusions + findings + summary + + conclusion section - + - - + + - - + + - transplantation - - a protocol application to replace an organ or tissue of an organism - PlanAndPlannedProcess Branch - OBI branch derived - transplantation + conflict of interest section + The section labelled 'conflict of interest statement' in a typical scientific journal article. + A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. + PERSON: Bill Baumgartner + competing interests + conflict of interest + conflict of interest statement + declaration of competing interests + disclosure of potential conflicts of interest + + conflict of interest section - + - - - 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. - Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 - - a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. - GROUP: Role Branch - OBI and Wikipedia - - obsolete biological vector role - true + + + conflict of interest statement + SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] + A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. + PERSON: Bill Baumgartner + + conflict of interest textual entity - + - - - pH indicator dye role - bromophenol blue has a pH indicator dye role - phenol red in RPMI; pH=4 indicator dye (also carries reference role) - - the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity - Person: Jennifer Fostel - Person:Helen Parkinson - pH indicator dye - pH indicator dye role + + + + + + + + + consent section + The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) + A part of a document about the consent process that was used to enroll patients in a study. + PERSON: Bill Baumgartner + consent + + consent section - + - - - - - - - - - - - - - - - - - - - specimen role - liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. - - a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation - 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - blood taken from animal: animal continues in study, whereas blood has role specimen. -something taken from study subject, leaves the study and becomes the specimen. - parasite example -- when parasite in people we study people, people are subjects and parasites are specimen -- when parasite extracted, they become subject in the following study -specimen can later be subject. - GROUP: Role Branch - OBI - - specimen role + + + consent textual entity + From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): + +Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. + A textual entity that documents the consenting process used to enroll patients in a study. + PERSON: Bill Baumgartner + + consent textual entity - + - - - sequence feature identification objective - - Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. - Jennifer Fostel - sequence feature identification objective + + + + + + + + + ethical approval section + The section labelled 'ethical approval' in a typical scientific journal article. + A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. + PERSON: Bill Baumgartner + ethical approval + + ethical approval section - + - - - - - - - - - - - - - - - - - - - - - - - intervention design - PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. - - An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. - Philppe Rocca-Serra - OBI branch derived - intervention design + + + + + + + + + ethical approval textual entity + From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): + +The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. + A textual entity that documents the ethical approval of some study design. + PERSON: Bill Baumgartner + + ethical approval textual entity - + - - - worker role - Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html - - a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline - "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study - Person:Jennifer Fostel - worker - OBI - worker role + + + + + + + + + figures section + The section labelled 'figures' in a typical scientific journal article. + A part of a document that contains one or more figures. + PERSON: Bill Baumgartner + figures + + figures section - + - - - - An assay where the output data is a datum with one of two values denoting success and failure. - PlanAndPlannedProcess Branch - OBI branch derived - Bernoulli trial + + + + + + + + + funding source declaration section + The section labelled 'funding' in a typical scientific journal article. + A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. + PERSON: Bill Baumgartner + funding + funding information + funding sources + funding statement + funding/support + source of funding + sources of funding + + funding source declaration section - + - - - gene list - Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. - - A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. - person:Chris Stoeckert - group:OBI - kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object. - gene list + + + funding souce declaration textual entity + From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): + +This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. + A textual entity documenting the source of funding that supported some study. + PERSON: Bill Baumgartner + + funding source declaration textual entity - + - - - number of particles in subset - 500, 200, 0 - - A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role - person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt - number of particles in subset + + + + + + + + + future directions section + The section labelled 'future directions' in a typical scientific journal article. + A part of a document detailing extensions of the described work that may be implemented at some future point in time. + PERSON: Bill Baumgartner + future challenges + future considerations + future developments + future directions + future outlook + future perspectives + future plans + future prospects + future research + future research directions + future studies + future work + + future directions section - + - - - number of lost events electronic - 74, 0, 14 events lost due to data acquisition electronic coincidence. - - A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. - person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt - number of lost events electronic + + + future directions textual entity + Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): + +In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. + A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. + PERSON: Bill Baumgartner + + future directions textual entity - + - - + + - - + + - calibration substance role - pH buffer used to calibrate a pH meter bears a calibration substance role - - A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance - Jennifer Fostel - calibration substance role + genome announcement section + The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) + A document part announcing the publication of a novel draft genome sequence. + PERSON: Bill Baumgartner + genome announcement + + genome announcement section - + - - - molecular feature identification objective - - Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. - Jennifer Fostel - molecular feature identification objective + + + genome announcement textual entity + Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): + +Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). + A textual entity that describes the generation and public release of a novel, draft genome sequence. + PERSON: Bill Baumgartner + + genome announcement textual entity - + - - - hardware testing objective - - Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. - Jennifer Fostel - hardware testing objective + + + keyword textual entity + From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): + +Exon orthology; alternative splicing; exon duplication; intron-exon structure. + A textual entity listing keywords indicating the major theme(s) of a document. + PERSON: Bill Baumgartner + + keyword textual entity - + - - + + - - + + - incubator - Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells - - A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled - Frank Gibson - http://www.medterms.com/script/main/art.asp?articlekey=18426 - incubator + keywords section + The section labelled 'keywords' in a typical scientific journal article. + A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. + PERSON: Bill Baumgartner + keywords + + keywords section - + - - - - Label role is a role which inheres in a material entity and which is realized in a detection of label assay - Role Branch - label - OBI - - - obsolete_label role - true + + + + + + + + + + + + + + + study limitations section + The section labelled 'limitations' in a typical scientific journal article. + A part of a document about biases or short comings related to the study design and execution. + PERSON: Bill Baumgartner + limitations + study limitations + Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) + + study limitations section - + - - - baseline participant role - Subject at time = 0; subject before a stress test. - - a reference participant role which is realized by making the reference to qualities at the start of the study or intervention - Person: Jennifer Fostel - baseline participant - baseline participant role + + + study limitations textual entity + Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). + +Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. + A textual entity addressing a shortcoming or bias of a study design or execution. + PERSON: Bill Baumgartner + Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) + + study limitations textual entity - + - - - role of independent data monitoring committee - - a trial monitor role charged recommending whether to continue, modify, or end the trial - Person: Jennifer Fostel - independent data monitoring committee - role of independent data monitoring committee + + + materials section + The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) + A part of a document about the materials required to reproduce the content of the document. + PERSON: Bill Baumgartner + materials + + materials section - + - - - pathologist role - - a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline - Person:Jennifer Fostel - Pathologist - pathologist role + + + notes section + The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): + A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. + PERSON: Bill Baumgartner + footnotes + notes + + notes section - + - - + + - - + + - supernatant collection system harvesting frame - - A device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. - Daniel Schober - google - supernatant collection system harvesting frame + patients section + The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) + A part of a document about the patients that participated in a study. + PERSON: Bill Baumgartner + + patients section - + - - - - - - - - - filter paper - - A device manufacture with the intent to provide a porous unsized paper used for filtering. - Frank Gibson - sep:00107 - filter paper + + + patients textual entity + Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): + +Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. + A textual entity expressing information regarding the patients used in a study. + PERSON: Bill Baumgartner + + patients textual entity - + - - - - - - - - - - - - 2 - - - - + + - - + + + pre-publication history section + The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) + A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. + PERSON: Bill Baumgartner + notice of republication + pre-publication history + + pre-publication history section + + + + + + + + + pre-publication history textual entity + From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): + +The pre-publication history for this paper can be accessed here: +http://www.biomedcentral.com/1471-2253/13/33/prepub + A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. + PERSON: Bill Baumgartner + + pre-publication history textual entity + + + + + + + + - - + + + related work section + The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) + A part of a document about work in other publications that is relevant to the content of the document. + PERSON: Bill Baumgartner + related literature + related work + + related work section + + + + + + + + + related work textual entity + Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): + +Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). + + + A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. + PERSON: Bill Baumgartner + + related work textual entity + + + + + + + + - - + + - cell co-culturing - Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay - - A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. - PlanAndPlannedProcess Branch - OBI branch derived - cell co-culturing + requirements section + The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). + A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. + PERSON: Bill Baumgartner + requirements + + requirements section - + - - - role of Institutional Review Board - An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008 - Animal protocol review board - - the role of a organization that is realized by members reviewing study designs for their agreement with regulations - Person:Helen Parkinson - Person:Jennifer Fostel - Internal Review Board - OBI, CDISC - CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial. - role of Institutional Review Board + + + requirements textual entity + From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): + +• Operating systems: Platform independent + +• Programming language: Matlab, R, Python + +• Other requirements: None + +• License: GNU GPL v3 + +• Any restrictions to use by non-academics: None + A textual entity that expresses the requirements necessary to use a resource, e.g. software. + PERSON: Bill Baumgartner + + requirements textual entity - + - - - eSource document - - an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures - person:Jennifer Fostel - article-without-pmid-or-doi:CDISCglossary - eSource document + + + statistical analysis textual entity + From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): + +Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. + A textual entity documenting statistical analysis tools and techniques employed. + PERSON: Bill Baumgartner + + statistical analysis textual entity - + - - - crossover population role - - a role realized when a participant serves as reference to itself - Person: Jennifer Fostel - crossover population - crossover population role + + + + + + + + + statistical analysis section + The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) + A part of the document used to describe the statistical methodologies employed in the work presented in the document. + PERSON: Bill Baumgartner + statistical analysis + + statistical analysis section - + - - - complete nutrient role - Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm - - A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. - Person: Jennifer Fostel - complete nutrient - complete nutrient role + + + + + + + + + tables section + The section labelled 'tables' in a typical scientific journal article. + A part of a document that contains one or more tables. + PERSON: Bill Baumgartner + tables + + tables section - + - - - radiolabel role - - a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection - Jennifer Fostel - radiolabel - radiolabel role + + + An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. + Mathias Brochhausen + postal code - + - - + + + A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. + Mathias Brochhausen + Postal delivery route + + + + + + + + + A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. + Mathias Brochhausen + ZIP code + zone improvement plan code + + + + + + + + - - + + - - + + - cDNA library - PMID:6110205. collection of cDNA derived from mouse splenocytes. - - Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. - -ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. - PERSON: Luisa Montecchi - PERSON: Philippe Rocca-Serra - GROUP: PSI - PRS: 22022008. class moved under population, -modification of definition and replacement of biomaterials in previous definition with 'material' -addition of has_role restriction - clonal cDNA library + database extract, transform, and load process + A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. + Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second + Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. + PERSON:Alan Ruttenberg + ETL + WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load + + + database extract, transform, and load process + - + - + - electronic case report form - - An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11. - person:Jennifer Fostel - CDISC glossary - electronic case report form + identifier + An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. + + identifier - + - - - placebo role - Pill consisting of inert materials - - a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance - Person:Jennifer Fostel - placebo - CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product. - placebo role + + + ontology module + I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. + ontology file + This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. + ontology module - + - - - autotransplantation - - is the transplantation of tissue from one part of \nthe body to another in the same individual. ) - PlanAndPlannedProcess Branch - OBI branch derived - autotransplantation + + + base ontology module + An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. + base ontology module + - + - - - parameter threshold - 0.01, 0.03 - - A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role - person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt - parameter threshold + + + editors ontology module + An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. + source ontology module + editors ontology module - + - - - study group role - The group of randomized participants that are assigned to a treatment arm of the trial - - a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol - Jennifer Fostel - study group population - study group role + + + main release ontology module + An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. + TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module + main release ontology module - + - - - p-value - PMID:19696660 -in contrast to the in-vivo data AT-III increased significantly from -113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2). - - A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. - May be outside the scope of OBI long term, is needed so is retained - PERSON:Chris Stoeckert - WEB: http://en.wikipedia.org/wiki/P-value - p-value + + + bridge ontology module + An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. + bridge ontology module + - + - - - population - PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. - - a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area - 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: -http://code.google.com/p/popcomm-ontology/ - PERSON: Philippe Rocca-Serra - adapted from Oxford English Dictionnary - rem1: collection somehow always involve a selection process - population + + + import ontology module + A subset ontology module that is intended to be imported from another ontology. + TODO: add axioms that indicate this is the output of a module extraction process. + import file + import ontology module + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013). - A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. - IEDB - PlanAndPlannedProcess Branch - IEDB - NMR 3D molecular structure determination assay + + + subset ontology module + An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. + ontology slim + subset ontology + subset ontology module + + - + - - - - - - - - - - An assay that produces a picture of an entity. - PlanAndPlannedProcess Branch - OBI branch derived - imaging assay + + + curation subset ontology module + A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. + curation subset ontology module - + - - - protocol optimization objective - - Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. - Jennifer Fostel - protocol optimization objective + + + analysis ontology module + An ontology module that is intended for usage in analysis or discovery applications. + analysis subset ontology module - + - - - role of pathology review board - - a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation - Person: Jennifer Fostel - pathology review board - role of pathology review board + + + single layer ontology module + A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. + ribbon subset + single layer subset ontology module - + - - - - - - - - - microtiter plate - A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) - - A microtiter_plate is a flat plate with multiple wells used as small test tubes. - Melanie Courtot - microplate - http://en.wikipedia.org/wiki/Microtiter_plate - microtiter plate + + + exclusion subset ontology module + A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. + antislim + exclusion subset ontology module - + - - - role of impartial witness - According to GCP , an impartial witness should be present for an -illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html - - a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial - impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who - Person: Helen Parkinson - Person: Jennifer Fostel - impartial witness - role of impartial witness + + + external import ontology module + An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. + external import + external import ontology module - + - - - Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method. - An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics. - Bjoern Peters, Randi Vita, James A. Overton - ChIP - OBI - chromatin immunoprecipitation + + + species subset ontology module + A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. + taxon subset + species subset ontology module + - + - - - biological replicate role - A member of a dose-time group; a patient in a given arm of a trial - - a reference participant role realized by equivalent treatment of participants - Person:Jennifer Fostel - biological replicate - OBI - biological replicate role + + + reasoned ontology module + An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. + reasoned ontology module + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. - An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. - IEDB - PlanAndPlannedProcess Branch - IEDB - radioactivity detection + + + generated ontology module + An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. + TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process + generated ontology module - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - investigation agent role - The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. - - A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. - Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. - Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) - GROUP: Role Branch - investigator - OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - study person role - Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) - investigation agent role + + + template generated ontology module + An ontology module that is automatically generated from a template specification and fillers for slots in that template. + template generated ontology module + + + - + - - - - - - - - - nutrient role - Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia. - - a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. - GROUP: Role branch - nutrient - Wikipedia, feb 29, 2008 - 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment. - nutrient role + + + taxonomic bridge ontology module + taxonomic bridge ontology module - + - - - Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study) - - Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. - Role Branch - OBI - - obsolete_dropout role - true + + + ontology module subsetted by expressivity + ontology module subsetted by expressivity - + - - - - a worker role of providing medical care either within or outside the study timeline - Person:Jennifer Fostel - health care provider - - obsolete health care provider role - true + + + obo basic subset ontology module + A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. + +Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). + +An ontology is OBO Basic if and only if it has the following characteristics: +DAG +Unidirectional +No Dangling Clauses +Fully Asserted +Fully Labeled +No equivalence axioms +Singly labeled edges +No qualifier lists +No disjointness axioms +No owl-axioms header +No imports + obo basic subset ontology module + - + - - - methodology testing objective - - Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. - Jennifer Fostel - methodology testing objective + + + ontology module subsetted by OWL profile + ontology module subsetted by OWL profile - + - - - analytical cytology data file - FCS file, ACS file, foo.fcs, foo.asc - - A digital entity intended to capture data in analytical cytology domain. - person:Chris Stoeckert - group:Flow Cytometry community - analytical cytology data file + + + EL++ ontology module + EL++ ontology module - + - - - proxy respondent role - - Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel - Jennifer Fostel - proxy respondent - proxy respondent role + + + pathogenic disposition + A disposition to initiate processes that result in a disorder. + + pathogenic disposition - + - - - fluorescence compensation matrix - ((1.053096, -0.22476), (-0.24877, 1.053096)) - - A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix. - person:Chris Stoeckert - group:Flow Cytometry community - fluorescence compensation matrix + + + pathogen + A material entity with a pathogenic disposition. + + pathogen - + - - - - - - - - - negative reference substance role - Saline solution - - a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response - Person: Jennifer Fostel - negative reference substance - negative reference substance role + + + antibacterial + A material entity bearing an antibacterial disposition. + + antibacterial - + - - - role of legally acceptable representative - Parent of minor patient; Definition of legally acceptable representative -An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE - - a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial. - legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary] - Person: Jennifer Fostel - Person:Helen Parkinson - legally acceptable representative - OBI, CDISC - role of legally acceptable representative + + + infection + A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. + + infection - + - - - investigation results report - - An investigation report is a report on the results of an investigation. - person:Chris Stoeckert - group:OBI - investigation results report + + + human pathogenicity disposition + A disposition to initiate processes that result in a disorder in a human organism. + + human pathogenicity disposition - + - - - cellular feature identification objective - - Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. - Jennifer Fostel - cellular feature identification objective + + + Mus musculus + house mouse + mouse + + Mus musculus - + - - - - - - - - - - - - - - - - reference subject role - Saline treated rat; one of three identically-treated subjects - - a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference - Jennifer Fostel - reference participant - OBI - reference subject role + + + Rattus norvegicus + Norway rat + brown rat + rat + rats + + Rattus norvegicus - + - - - vital dye role - typtan blue has a vital dye - - A dye role that is realized when used to detect live cells in an experiment - 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178 - Person: Helen Parkinson - Person: Jennifer Fostel - vital dye - vital dye role + + + Viruses + + Viruses - + - - - 115 patients received ipilimumab and blinded medication - Inert pill shaped like aspirin tablet - - Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance - Jennifer Fostel - Person:Helen Parkinson - - obsolete_blinded medication role - true + + + Herpesviridae + + Herpesviridae - + - - - sub-investigator role - - a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline - Person: Jennifer Fostel - sub-investigator - CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows - sub-investigator role + + + Cytomegalovirus + + Cytomegalovirus - + - - - data encoding - storage of measurement results from an assay into a text file, such as - - a documenting process to encode an information entity into a digital document - PlanAndPlannedProcess Branch - OBI branch derived - We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE - data encoding + + + Human gammaherpesvirus 4 + Epstein Barr virus + Epstein-Barr virus + Epstein-Barr virus EBV + Human herpesvirus 4 + Human herpesvirus type 4 + + Human gammaherpesvirus 4 - + - - - - - - - - - - - - - - - - - - - - - - - - - enzymatic cleavage - Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828 - - a material processing that digests the fraction of input material that is susceptible to that enzyme - PlanAndPlannedProcess Branch - OBI branch derived - enzymatic cleavage + + + Hepatitis B virus + Human hepatitis B virus + hepatitis B virus (HBV) + hepatitis B virus HBV + hepatitis B virus, HBV + human hepatitis B virus HBV + + Hepatitis B virus - + - - - hardware optimization objective - - Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. - Jennifer Fostel - hardware optimization objective + + + Hepacivirus C + Hepatitis C virus + hepatitis C virus HCV + human hepatitis C virus + human hepatitis C virus HCV + human hepatitis virus C HCV + post-transfusion hepatitis non A non B virus + + Hepacivirus C - + - - - - Place holder class, Utility class to gather the defined classes - Susanna Sansone - OBI Biomaterial derived - - obsolete_defined_material - true + + + Lentivirus + Lentivirinae + + Lentivirus - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - trial statistician role - - a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. - Person:Jennifer Fostel - trial statistician - CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9] - trial statistician role + + + Human immunodeficiency virus 1 + human immunodeficiency virus 1 HIV-1 + human immunodeficiency virus HIV-1 + human immunodeficiency virus type 1 HIV 1 + human immunodeficiency virus type 1 HIV1 + human immunodeficiency virus type 1, HIV-1 + human immunodeficiency virus type I HIV-1 + human immunodeficiency virus type-1 HIV-1 + human immunodeficiency virus-1 HIV-1 + + Human immunodeficiency virus 1 - + - - - standard error - - A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. - person:Chris Stoeckert - group:OBI - see P-Value - standard error + + + Human immunodeficiency virus 2 + HIV type 2 + Human immunodeficiency virus type 2 + Human immunodeficiency virus-2 + human immunodeficiency virus type 2 HIV-2 + human immunodeficiency virus type 2, HIV-2 + + Human immunodeficiency virus 2 - + - - - - - - - - - antigen role - - Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response - An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens - Role Branch - OBI - 9Mar09 waiting for discussion with immunology terms - antigen role + + + Euteleostomi + bony vertebrates + + Euteleostomi - + - - - software testing objective - - Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. - Jennifer Fostel - software testing objective + + + Ecdysozoa + + Ecdysozoa - + - - - sponsor role - - a responsible party role involved with any of the following activities: initiating, managing and funding a study - Person: Jennifer Fostel - sponsor - CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators - sponsor role + + + Treponema pallidum + + Treponema pallidum - + - - - organization - PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. - - An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. - BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + + + Pancrustacea + + Pancrustacea + + -1) there are organization_member_roles (president, treasurer, branch -editor), with individual persons as bearers -2) there are organization_roles (employer, owner, vendor, patent holder) + -3) an organization has a charter / rules / bylaws, which specify what roles -there are, how they should be realized, and how to modify the -charter/rules/bylaws themselves. + + + Bacteria + eubacteria + + Bacteria + + -It is debatable what the organization itself is (some kind of dependent -continuant or an aggregate of people). This also determines who/what the -bearer of organization_roles' are. My personal favorite is still to define -organization as a kind of 'legal entity', but thinking it through leads to -all kinds of questions that are clearly outside the scope of OBI. -Interestingly enough, it does not seem to matter much where we place -organization itself, as long as we can subclass it (University, Corporation, -Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, -W3C, University of Oklahoma), and have it play roles. + -This leads to my proposal: We define organization through the statements 1 - -3 above, but without an 'is a' statement for now. We can leave it in its -current place in the is_a hierarchy (material entity) or move it up to -'continuant'. We leave further clarifications to BFO, and close this issue -for now. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra - PERSON: Susanna Sansone - GROUP: OBI - organization + + + Archaea + + Archaea - + - - - feed role - Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008 - - a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. - Person: Jennifer Fostel - feed - OBI - feed role + + + Riboviria + RNA viruses + RNA viruses and viroids + + Riboviria - + - - - technical replicate role - Aliquots of a tissue subjected to parallel assays - - technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay - Person: Jennifer Fostel - technical replicate - technical replicate role + + + Revtraviricetes + + Revtraviricetes - + - - - dye role - - A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. - Jennifer Fostel - dye - A substance used to color materials www.answers.com/topic/dye 19feb09 - dye role + + + Eukaryota + eucaryotes + eukaryotes + + Eukaryota - + - - - cluster - Cluster of the lymphocytes population. - - A data set which is a subset of data that are a similar to each other in some way. - person:Allyson - person:Chris Stoeckert - group:OBI - cluster + + + Euarchontoglires + + Euarchontoglires - + - - - cohort role - In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008 - - a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study. - Jennifer Fostel - WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students. - WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site). - WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation. - cohort role + + + Tetrapoda + tetrapods + + Tetrapoda - + - - - - - - - - - artificially induced nucleic acid hybridization - www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf - - Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules. - PlanAndPlannedProcess Branch - OBI branch derived - artificially induced nucleic acid hybridization + + + Amniota + amniotes + + Amniota - + - - - - - - - - - DNA extraction - - A DNA extraction is a nucleic acid extraction where the desired output material is DNA. - PlanAndPlannedProcess Branch - OBI branch derived - DNA extraction + + + Opisthokonta + + Opisthokonta - + - - - plan - The plan of researcher X to perform an experiment according to a protocol. - - A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. - This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. - AR, BP, JM, MC, PRS - branch derived - plan + + + Metazoa + metazoans + multicellular animals + + Metazoa - + - - - Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 - - A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. - PERSON: Jennifer Fostel - PERSON: Philippe Rocca-Serra - recruited population - GROUP: OBI Biomaterial Branch - - obsolete_sample population - true + + + Bilateria + + Bilateria - + - - - organism feature identification objective - - Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. - Jennifer Fostel - organism feature identification objective + + + Arabidopsis thaliana + mouse-ear cress + thale cress + thale-cress + + Arabidopsis thaliana - + - - - number of lost events computer - 0, 125, 787 events lost due to computer busy. - - A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role - person:Kevin Clancy - Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt - number of lost events computer + + + HIV-1 group O + + HIV-1 group O - + - - - protocol - PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. - - A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. - PlanAndPlannedProcess Branch - OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) - study protocol - protocol + + + Murinae + + Murinae - + - - - role of regulator of consumables and medical devices - FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html - - a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices - Person: Jennifer Fostel - drug regulatoy authority - OBI, CDISC - role of regulator of consumables and medical devices + + + Mammalia + mammals + + Mammalia - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - adding a material entity into a target - Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. - - is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. - Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. - BP - branch derived - adding a material entity into a target + + + Dictyostelium discoideum + + Dictyostelium discoideum - + - - - - - - - - - - - - - - - - analyte role - Glucose in blood (measured in an assay to determine the concentration of glucose). - - A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. - interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role - pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. - qualities such as weight, color are not assayed but measured, so they do not fall into this category. - GROUP: Role Branch - OBI - Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - analyte role + + + Ascomycota + ascomycetes + sac fungi + + Ascomycota - + - - - - - - - - - disease stage - Stage II breast cancer, The timepoint of recovery from a disease - - a part of an occurrence of a disease process which is associated with position in the normal progression of the disease - PERSON: Bjoern peters - disease stage + + + Schizosaccharomyces pombe + fission yeast + + Schizosaccharomyces pombe - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intraperitoneal injection - - is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe - BP - intraperitoneal injection + + + Saccharomyces cerevisiae + S. cerevisiae + baker's yeast + brewer's yeast + + Saccharomyces cerevisiae - + - - - - - - - - - precipitate - Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038 - - a precipitate is a material entity which is output of a precipitation process - PERSON: Philippe Rocca-Serra - precipited material - GROUP: OBI Biomaterial Branch - precipitate + + + Neurospora + + Neurospora - + - - - - An assay that determines interactions between proteins, such as protein-protein binding. - protein-protein interaction detection assay + + + Plasmodium + + Plasmodium - + - - - - - - - - - - - - - - - - - - - - Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. - - An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors - Philippe Rocca-Serra - TF binding - OBI - https://sourceforge.net/p/obi/obi-terms/767/ - transcription factor binding site assay + + + Caenorhabditis elegans + + Caenorhabditis elegans - + - - - Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 - - enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules - Bjoern Peters - IEDB - - obsolete_enrollment - true + + + Arthropoda + arthropods + + Arthropoda - + - - - adverse event trigger - - revisit? - PERSON:Alan Ruttenberg - OBI branch derived - adverse event trigger + + + Daphnia + common water fleas + + Daphnia - + - - - - - - - - - - - - - - - - - - - - - - - - - eluate - Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263 - - a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase - need to add restriction to indicate: has_part some (material entity has_role mobile phase) -need to add mobile phase as role - PERSON: Philippe Rocca-Serra - eluted material - OBI Bionaterial - eluate + + + Diptera + flies + + Diptera - + - - - material to be added role - drug added to a buffer contained in a tube; substance injected into an animal; - - material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process - Role Branch - OBI - 9 March 09 from discussion with PA branch - material to be added role + + + Culicidae + mosquitos + + Culicidae - + - - - - is the serous membrane that forms the lining of the abdominal cavity - - obsolete_peritoneum - true + + + saccharomyceta + + saccharomyceta - + - - - - - - - - - - - - - - - interpreting data - Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. - - A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - Bjoern Peters - drawing a conclusion based on data + + + Drosophila melanogaster + fruit fly + + Drosophila melanogaster - + - - - - - - - - - - - - - planning - The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. - - a process of creating or modifying a plan specification - 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. - Bjoern Peters - Bjoern Peters - Plans and Planned Processes Branch - planning + + + Vertebrata <vertebrates> + Vertebrata + vertebrates + + Vertebrata <vertebrates> - + - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting - - - obsolete_documenting - true + + + Danio rerio + leopard danio + zebra danio + zebra fish + zebrafish + + Danio rerio - + - - - - - - - - - - - - - - - - - - - - - - - - - - - histological sample preparation - - histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay - PERSON:Bjoern Peters - OBI branch derived - histological sample preparation + + + Xenopus <genus> + Xenopus + + Xenopus <genus> - - - - - inductive reasoning - Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer. - - a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. - BP: 10/22/122: After changing the parent class to drawing a conclusion *based on data* it is no longer clear that this class is needed; minimally it needs a better definition to distinguish it. - -Proposal is to obsolete. + - - Bjoern Peters - wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning - inductive reasoning + + + Gallus gallus + Gallus domesticus + bantam + chicken + chickens + + Gallus gallus - + - - - - - - - - - - - - - - - mass analyzer - The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation - - A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. - Frank Gibson - PERSON: Daniel Schober - http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer - mass analyzer + + + Homo sapiens + human + human being + + Homo sapiens - + - - - hypothesis driven investigation - - is an investigation with the goal to test one or more hypothesis - PlanAndPlannedProcess Branch - OBI branch derived - hypothesis driven investigation + + + Rodentia + rodent + + Rodentia - + - - - hypothesis generating investigation - - is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis - PlanAndPlannedProcess Branch - OBI branch derived - hypothesis generating investigation + + + role of being consumer safety officer + Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm + Person charged with serving as CSO, FDA official who coordinates the review + + the role of a human being that is realized by enforcing regulations to ensure consumer safety + Jennifer Fostel + Person:Helen Parkinson + OBI, CDISC + role of being consumer safety officer - + - - - - - - - - - ion source - The ion source of a Voyager-DE??? STR Biospectrometry Workstation - - An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). - Frank Gibson - http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source - ion source + + + fluorescent reporter intensity + + A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. + person:Chris Stoeckert + group:OBI + From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem. + fluorescent reporter intensity - + - - - + + - - + + + + + + + - - ion detector - The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation + + + planned process + planned process + Injecting mice with a vaccine in order to test its efficacy - An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. - Frank Gibson - http://en.wikipedia.org/wiki/Mass_spectrometry#Detector - ion detector + A process that realizes a plan which is the concretization of a plan specification. + 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process. + Bjoern Peters + branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + planned process - + - - - - - - - - - Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 + + + regulator role + Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 - An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism - Philippe Rocca-Serra - metabolite assay - metabolomic assay - OBI - metabolite profiling assay + a regulatory role involved with making and/or enforcing relevant legislation and governmental orders + Person:Jennifer Fostel + regulator + OBI + regulator role - + - - - light emission function - - A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - light emission function + + + biological feature identification objective + + Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. + Jennifer Fostel + biological feature identification objective - + - - - record function - - A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - record function + + + regulation-assigned role + Approval letter + + Regulation-assigned role is a regulatory role defined by legislation or governmental orders + Person: Jennifer Fostel + regulation-assigned role - + - - - magnify function - - A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - magnify function + + + regulatory role + Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 + + a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. + GROUP: Role branch + OBI, CDISC + govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent + regulatory role - + - - - contain function - A syringe, a beaker - - A contain function is a function to constrain a material entities location in space - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - contain function + + + material supplier role + Jackson Labs is an organization which provide mice as experimental material + + a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. + Supplier role is a special kind of service, e.g. biobank + PERSON:Jennifer Fostel + material provider role + supplier + material supplier role - + - - - heat function - - A heat function is a function that increases the internal kinetic energy of a material - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - heat function + + + contract research organization role + + a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution + Person: Jennifer Fostel + contract research organization + contract research organization role - + - - - material separation function - - A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - material separation function + + + list-mode data file + An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used. + + A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter. + One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people. + person:Chris Stoeckert + group:Flow Cytometry community + list-mode data file - + - - - - - - - - - - - - - - - + + - - + + - - ionize process - Electrospray ionization in mass spectrometry - - a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation. - 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize - Person:Bjoern Peters - ionize process - - - - - - - - - excitation function - - A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - excitation function + + + classified data set + + A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. + PERSON: James Malone + PERSON: Monnie McGee + data set with assigned class labels + classified data set - + - - - freeze function - - A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - freeze function + + + + + + + + + reference substance role + Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html + + a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. + Person:Jennifer Fostel + reference substance + OBI + reference substance role - + - - - synthesizing function - - A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - synthesizing function + + + cytological stain role + haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin + + A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization + Person:Helen Parkinson + Person:Jennifer Fostel + cytological stain + cytological stain role - + - - - perturb function - - A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - http://en.wikipedia.org/wiki/Perturbation_biology - perturb function + + + + + + + + + + + + + + + centrifuge pellet role + Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet + + pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.. + GROUP: Role branch + OBI + 9Mar09 after discussion with process branch changed definition to include use of centrifuge; + centrifuge pellet role - + - - - filter function - - A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through - Frank Gibson - filter function + + + clinical research coordinator role + + a worker role comprised of handling the administrative duties of a trial or study. + Person:Jennifer Fostel + clinical research coordinator + clinical research coordinator role - + - - - mechanical function - - A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - http://en.wikipedia.org/wiki/Mechanical_work - mechanical function + + + + + + + + + + + + + + + supernatant role + Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia + + supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material. + GROUP: Role branch + OBI + supernatant role - + - - - gas filter function - - A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture - Frank Gibson - gas filter function + + + + + + + + + + + + + + + + + + + + + + + + + chromatography column + + Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. + Frank Gibson + http://en.wikipedia.org/wiki/Column_chromatography + open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 + chromatography column - + - - - liquid filter function - - A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture - Frank Gibson - liquid filter function + + + + + + + + + drug role + http://www.answers.com/topic/drug + 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. + 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act. + + a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism + Role Branch + drug + OBI, CDISC + drug role - + - - - transfer function - - A transfer function is a function to displace a material from one location to another. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - transfer function + + + + + + + + + pump valve switch + + A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. + FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument + OBI Instrument branch + OBI + pump valve switch - + - - - electricity supply function - the function of supplying current during a neuroscience experiment. - - An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment. - Daniel Schober - Frank Gibson - Melanie Courtot - power supply - electricity supply function + + + xenotransplantation + + is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans + PlanAndPlannedProcess Branch + OBI branch derived + xenotransplantation - + - - - ionization function - The ion source in amass spectrometer - - An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - http://en.wikipedia.org/wiki/Ionization - ionization function + + + physical document + a book is a physical document + + A physical document is an object serving as a record of information by means of symbolic marks. + PERSON: Bjoern Peters + GROUP: OBI + physical document - + - - - cool function - - A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. - Daniel Schober - Frank Gibson - Melanie Courtot - cool function + + + waiting + + not actively doing anything to a material for a duration of time. + PERSON:Alan Ruttenberg + OBI branch derived + BP: I have doubts about the utility of this. + We need a better handling/modeling of time (January 2008) + waiting - + - - - connection function - An electricity cable + + + + + + + + + + + + + processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - connection function + Is a material entity that is created or changed during material processing. + PERSON: Alan Ruttenberg + processed material - + - + @@ -7775,7 +13813,7 @@ Proposal is to obsolete. - + @@ -7784,1419 +13822,945 @@ Proposal is to obsolete. - isoelectric focusing device + + + + + + + chromatography device - An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated. - Frank Gibson - isoelectric focusing unit - sep:00097 - isoelectric focusing device + A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. + Frank Gibson + chromatography instrument + http://en.wikipedia.org/wiki/Chromatography + open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 + chromatography device - + - + - - + + - - + + - thermostatic circulator - - A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid - Frank Gibson - sep:00098 - thermostatic circulator - - - - - - - - - energy supply function - - An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy - Frank Gibson - energy supply function - - - - - - - - - + - - + + - information processor function + mass spectrometer + LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific - An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. - Frank Gibson - data processor function - information processor function + A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum + Frank Gibson + http://en.wikipedia.org/wiki/Mass_spectrometry + mass spectrometer - + - - - signal conversion function - - A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - transduction function - signal conversion function + + + obsolete_platform + + A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. + OBI Instrument branch + OBI Instrument branch + + obsolete_platform + true - + - + + + + + + + + + + + + + - + + + + + + + - blot module + liquid chromatography mass spectrometry platform - A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised - Frank Gibson - sep:00092 - blot module - - - - - - - - - signal amplification function - - A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - signal amplification function + A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. + OBI instrument branch + OBI Instrument branch + liquid chromatography mass spectrometry platform - + - - + + - - + + - - + + - image acquisition function - - An image acquisition function is a function to acquire an image of a material - Frank Gibson - image acquisition function + microarray platform + + A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. + OBI Instrument branch + OBI Instrument branch + microarray platform - + - - - - - - - - - - - - - image acquisition device - - An image creation device is a device which captures a digitized image of an object - Frank Gibson - image acquisition device - sep:00096 - image creation device - - - - - - - - - solid support function - Taped, glued, pinned, dried or molecularly bonded to a solid support - - A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement - Daniel Schober - Frank Gibson - Melanie Courtot - solid support function + + + ratio of collected to emitted light + 10% + + A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role + person:Chris Stoeckert + person:Kevin Clancy + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + ratio of collected to emitted light - + - - - display function - - A display function is a function to present information by translating that information through some lookup process into visual form. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - display function + + + software optimization objective + + Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. + Jennifer Fostel + software optimization objective - + - - - environment control function - - An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. - Bill Bug - Daniel Schober - Frank Gibson - Melanie Courtot - environment control function + + + notified body role + The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf + + Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive + Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB. + Person: Jennifer Fostel + notified body + OBI, CDISC + notified body role - + - - - sort function - - A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. - Daniel Schober - Frank Gibson - Melanie Courtot - sort function + + + allotransplantation + + is the transplantation of organs between members of the same species. + PlanAndPlannedProcess Branch + OBI branch derived + allotransplantation - + - + - - - - - - - + - gel dryer - - A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels - Frank Gibson - sep:00094 - gel dryer + gamma counter + A Geiger counter + + A processed material which measures gamma radiation + Frank Gibson + http://en.wikipedia.org/wiki/Gamma_counter + gamma counter - + - - + + + trial monitor role + + a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study + Person:Jennifer Fostel + trial monitor + CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study. + trial monitor role + + + + + + + + - + - primer role + positive reference substance role + MMS mutagen - a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. - (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer - primer role + a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response + Person: Jennifer Fostel + positive reference substance + positive reference substance role - + - - - - - - - - - - - - - PCR product - PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. - - is double stranded DNA that is the specified output of a polymerase chain reaction - We are using PCR and not the written out words, as this is the most common used. - GROUP: OBI BIomaterial Branch - GROUP: OBI BIomaterial Branch - PCR product + + + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether + PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. + + triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties + Philippe Rocca-Serra + adapted from Wikipedia before possible import from CHEBI + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether - + - - + + - - + + - viral RNA extraction - The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703 - - The extraction of RNA from an input material that specifically isolates viral RNA - Person:Bjoern Peters - viral RNA extraction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + investigation + Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation + + a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). + Bjoern Peters + OBI branch derived + Could add specific objective specification + Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core +editor = PRS + + study + investigation - + - - + + - + - + - nucleic acid template role - a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 - - a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. - nucleic acid template role + evaluant role + When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. + + a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role + Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) + examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") + GROUP: Role Branch + OBI + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + evaluant role - + - - - - - - - - - - - - - recombinant plasmid + + + reporting party role + Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. + The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm - a plasmid in which extraneous DNA has been inserted. - PERSON: Bjoern Peters - PERSON: Kevin Clancy - PERSON: Melanie Courtot - GROUP: OBI Biomaterial Branch - recombinant plasmid - - - - - - - - - - - - - - - - - - - - - - - cloning vector role - pBluescript plays the role of a cloning vector - - A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. - JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/ - PERSON: Helen Parkinson - cloning vector role + a study personnel role played by a party who reports the outcome of a study component + MO:submitter mapped to this term. So, alternative term 'submitter' was added. + Jennifer Fostel + reporting party + submitter + OBI + reporting party role - + - - - - - - - - - + + - - + + - + + - - + + - cell cycle synchronization - Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs. - - a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle - OBI PA - Bjoern Peters and Nicole Washington - cell cycle synchronization - - - - - - - - - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - polymerase chain reaction - Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 - - PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. - OBI Plan - PCR - adapted from wikipedai - polymerase chain reaction + + + + assay + Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. + + A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + PlanAndPlannedProcess Branch + measuring + scientific observation + OBI branch derived + study assay + any method + assay - + - - - cloning insert role - - cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. - Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" - GROUP: Role branch - OBII and Wikipedia - cloning insert role + + + quantitative confidence value + + A data item which is used to indicate the degree of uncertainty about a measurement. + person:Chris Stoeckert + group:OBI + quantitative confidence value - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319. - - An assay that determines the concentration of glucose molecules in a blood serum sample - Bjoern Peters - OBI - measuring glucose concentration in blood serum assay + sample preparation for assay + + A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. + PlanAndPlannedProcess Branch + study + OBI branch derived + sample preparation for assay - + - - - - - - - - - - - - - - - - - - reverse transcriptase - - enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase -activity) - person:Melanie Courtot - group:OBI - reverse transcriptase + + + diagnosis textual entity + + diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. + Jennifer Fostel + diagnosis textual entity - + - - - A trypsinized suspension of cells - - A material entity that has undergone a process of digestion with trypsin - Person:Bjoern Peters - - obsolete_trypsinized material - true + + + unplanned occurrence effecting an investigation + Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used + + a process which is external in origin to the investigation that has an impact on the outcome. + PERSON: Bjoern Peters + OBI + unplanned occurrence effecting an investigation - + - - - - - - - - - syringe - Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 - - A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw - Philippe Rocca-Serra - OBI Instrument adapted from Wikipedia - syringe + + + eMedical record + + An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. + person:Jennifer Fostel + article-without-pmid-or-doi:CDISCglossary + eMedical record - + - + - - - - - - - extract - Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 - - an extract is a material entity which results from an extraction process - PERSON: Philippe Rocca-Serra - extracted material - GROUP: OBI Biomatrial Branch - extract + culture medium + A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 + + a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. + changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 +Modification made by JZ. + Person: Jennifer Fostel, Jie Zheng + OBI + culture medium - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 + + + electronic case report tabulation - An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. - This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term. - Philippe Rocca-Serra - gene expression profiling - transcription profiling - OBI - transcription profiling assay + An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators. + person:Jennifer Fostel + CDISC glossary + electronic case report tabulation - + - - - averaging objective - A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. + + + polystyrene tube + Polystyrene tubes can be used to contain tissue culture cells during centrifgation - An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. - Elisabetta Manduchi - James Malone - PERSON: Elisabetta Manduchi - averaging objective + A polystyrene tube is a test tube made of polystyrene + PERSON: Chris Stoeckert + PERSON: Chris Stoeckert + polystyrene tube - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - injection - Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712 + + + reagent role + Buffer, dye, a catalyst, a solvating agent. - injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. - Philippe Rocca-Serra - OBI Biomaterial - injection + A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. + PERSON:Matthew Brush + reagent + PERSON:Matthew Brush + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + +May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. + + (copied from ReO) +Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. + +Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. + +In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). + reagent role - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - enzyme - - (protein or rna) or has_part (protein or rna) and -has_function some GO:0003824 (catalytic activity) - MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything -that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. - person: Melanie Courtot - GROUP:OBI - enzyme + + + role of regulator of chemical manufacturer + EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm + + a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture + Person: Jennifer Fostel + regulator of chemical manufacture + OBI + role of regulator of chemical manufacturer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intraperitoneal administration - Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h + + + detector reagent role - The administration of a substance into the peritoneum of an organism - Person:Bjoern Peters - intraperitoneal administration + a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. + 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances + One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009 + detector reagent role - + - - - - - - - - - - - - - - - - - - - - - - plasmid - - plasmid = DNA and has_quality circular and has_function -(is_realized_as some gene expression) GO:0010467 - person:Melanie Courtot - group:OBI - plasmid + + + role of certified IRB professional + CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional + + a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA + Person:Helen Parkinson + Person:Jennifer Fostel + certified IRB professional + WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional + role of certified IRB professional - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - injection into organ section - Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology - - A process in which an input substance is injected into a organ section. - Person:Bjoern Peters - injection into organ section + patient role + a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 + + a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider + GROUP:Role Branch + patient + OBI, CDISC + CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably + patient role - + - - + + + + + + + + - - + + - - + + - polyacrylamide gel - Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143 - - a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution - PERSON: Jie Zheng - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial Branch - polyacrylamide gel + + material processing + A cell lysis, production of a cloning vector, creating a buffer. + + A planned process which results in physical changes in a specified input material + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca Serra + material transformation + OBI branch derived + material processing - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + protocol testing objective + + Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols. + Jennifer Fostel + protocol testing objective + + + + + + + + - - + + - genotyping using an Affymetrix chip - - An assay with the objective to determine a sequence feature of DNA - Bjoern Peters - Philippe Rocca-Serra - OBI - DNA sequence feature detection assay + study subject role + Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. +Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. +Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. + + A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. + A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. + GROUP: Role Branch + OBI + Following OBI call November 2012,26th: + +1. it was decided there was no need for moving the children class and making them siblings of study subject role. +2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study + +This note closes the issue and validates the class definition to be part of the OBI core +editor = PRS + + participant under investigation role - + - - - adding material objective - creating a mouse infected with LCM virus - - is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity - BP - adding material objective + + + obsolete_role of being first subject treated + Rat 1A; first enrolled patient to receive treatment + + First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study + Role Branch + OBI + + obsolete_role of being first subject treated + true - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 + + + measured expression level + Examples are quantified data from an expression microarray experiment, PCR measurements, etc. - An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. - Philippe Rocca-Serra - SNP analysis - genotype profiling - OBI Biomaterial - genotyping assay + A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. + person:Chris Stoeckert + OBI Data Transformation branch + measured expression level - + - - - - - - - - - needle - Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569 + + + responsible party role + he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm - A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. - Philippe Rocca-Serra - OBI Instrument - needle + a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study + Person: Jennifer Fostel + responsible party + OBI + responsible party role - + - - - analyte measurement objective - The objective to measure the concentration of glucose in a blood sample - - an assay objective to determine the presence or concentration of an analyte in the evaluant - PERSON: Bjoern Peters - PPPB branch - analyte measurement objective + + + principal investigator role + + a responsible party role played by a person responsible for the overall conduct of a study + Person: Jennifer Fostel + principal investigator + CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC) + principal investigator role - + - - - - - - - - - - - - - - + + - + - Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 - - An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. - Philippe Rocca-Serra - OBI Biomaterial - DNA sequence variation detection assay + transplantation + + a protocol application to replace an organ or tissue of an organism + PlanAndPlannedProcess Branch + OBI branch derived + transplantation - + - - - - - - - - - agarose gel - Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269 + + + obsolete biological vector role + 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. + Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 - a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial Branch - agarose gel - - - - - - - - - assay objective - the objective to determine the weight of a mouse. - - an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) - PPPB branch - PPPB branch - assay objective + a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. + GROUP: Role Branch + OBI and Wikipedia + + obsolete biological vector role + true - + - - - Alan Ruttenberg's heart - - The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions - Person:Bjoern Peters - http://en.wikipedia.org/wiki/Heart - - obsolete_heart - true + + + pH indicator dye role + bromophenol blue has a pH indicator dye role + phenol red in RPMI; pH=4 indicator dye (also carries reference role) + + the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity + Person: Jennifer Fostel + Person:Helen Parkinson + pH indicator dye + pH indicator dye role - + - - - - - - - - + + - - + + + + + + + + + + + + - example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output + specimen role + liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. - An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. - Alan Ruttenberg - Bjoern Peters - Helen Parkinson - Philippe Rocca-Serra - Alan Ruttenberg - Bjoern Peters - Helen Parkinson - OBI Planned process branch - Philippe Rocca-Serra - analyte assay + a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation + 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + blood taken from animal: animal continues in study, whereas blood has role specimen. +something taken from study subject, leaves the study and becomes the specimen. + parasite example +- when parasite in people we study people, people are subjects and parasites are specimen +- when parasite extracted, they become subject in the following study +specimen can later be subject. + GROUP: Role Branch + OBI + + specimen role - + - - - - - - - - - - - - - - - target of material addition role - peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. - - target of material addition role is a role realized by an entity into which a material is added in a material addition process - From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. - GROUP: Role Branch - OBI - target of material addition role + + + sequence feature identification objective + + Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. + Jennifer Fostel + sequence feature identification objective - + - - - + + + - - - - - - - - - - - - - - - + - + - - + + @@ -9204,1884 +14768,1801 @@ that has_part some material entity is a material entity. If we add as equivalent - - - - - - - - The patients was weighed and mass was determined to be 47 kilograms + + intervention design + PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. + + An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. + Philppe Rocca-Serra + OBI branch derived + intervention design + + + + + + + + + worker role + Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html - An assay that determines the mass of an evaluant - Helen Parkinson - OBI - mass measurement assay + a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline + "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study + Person:Jennifer Fostel + worker + OBI + worker role - + - - - DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 - - a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval - Philippe Rocca-Serra - - obsolete_identification - true + + + Bernoulli trial + + An assay where the output data is a datum with one of two values denoting success and failure. + PlanAndPlannedProcess Branch + OBI branch derived + Bernoulli trial - + - - - - - - - - - - - - - - - - - - - - - An electrophysiology recording assay where the recording location of the electrode is intracellular - Frank Gibson - Frank Gibson - intra cellular electrophysiology recording assay + + + gene list + Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. + + A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. + person:Chris Stoeckert + group:OBI + kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object. + gene list - + - - - packed column + + + number of particles in subset + 500, 200, 0 - A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. - PERSON:Daniel Schober - WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218 - packed column + A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role + person:Kevin Clancy + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + number of particles in subset - + - - - example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. - - This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. - PERSON: Alan Ruttenberg - PERSON: James Malone - PERSON: Melanie Courtot - - obsolete_defined_output - true + + + number of lost events electronic + 74, 0, 14 events lost due to data acquisition electronic coincidence. + + A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role. + person:Kevin Clancy + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + number of lost events electronic - + - - - - - - - - - - - - - regulatory agency - The US Environmental Protection Agency + + + + + + + + + calibration substance role + pH buffer used to calibrate a pH meter bears a calibration substance role - A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. - GROUP: OBI Biomaterial Branch - WEB: en.wikipedia.org/wiki/Regulator - regulatory agency + A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance + Jennifer Fostel + calibration substance role - + - - - - - - - - - normalized data set - - A data set that is produced as the output of a normalization data transformation. - PERSON: James Malone - PERSON: Melanie Courtot - normalized data set + + + molecular feature identification objective + + Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. + Jennifer Fostel + molecular feature identification objective - + - - - - - - - - - - - - - - - - - - - - measure function - A glucometer measures blood glucose concentration, the glucometer has a measure function. - - Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. - PERSON: Daniel Schober - PERSON: Helen Parkinson - PERSON: Melanie Courtot - PERSON:Frank Gibson - measure function + + + hardware testing objective + + Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. + Jennifer Fostel + hardware testing objective - + - - - - - - - - + + - - - - - - - + + - The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron + incubator + Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells - An electrophysiology recording assay where the recording location of the electrode is extracellular - Frank Gibson - Helen Parkinson - Frank Gibson - extracellular electrophysiology recording assay + A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled + Frank Gibson + http://www.medterms.com/script/main/art.asp?articlekey=18426 + incubator - + - - - - - - - - - consume data function - - Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. - PERSON: Daniel Schober - PERSON: Frank Gibson - PERSON: Melanie Courtot - consume data function + + + obsolete_label role + + Label role is a role which inheres in a material entity and which is realized in a detection of label assay + Role Branch + label + OBI + + + obsolete_label role + true - + - - - material transformation objective - The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. - - an objective specifiction that creates an specific output object from input materials. - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - artifact creation objective - GROUP: OBI PlanAndPlannedProcess Branch - material transformation objective + + + baseline participant role + Subject at time = 0; subject before a stress test. + + a reference participant role which is realized by making the reference to qualities at the start of the study or intervention + Person: Jennifer Fostel + baseline participant + baseline participant role - + - - - - - - - - - - - - - - - - - - - - - manufacturing - - Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process - Manufacturing implies reproducibility and responsibility AR - This includes a single scientist making a processed material for personal use. - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - GROUP: OBI PlanAndPlannedProcess Branch - manufacturing + + + role of independent data monitoring committee + + a trial monitor role charged recommending whether to continue, modify, or end the trial + Person: Jennifer Fostel + independent data monitoring committee + role of independent data monitoring committee - + - - - manufacturing objective - - is the objective to manufacture a material of a certain function (device) - PERSON: Bjoern Peters - PERSON: Frank Gibson - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra - GROUP: OBI PlanAndPlannedProcess Branch - manufacturing objective + + + pathologist role + + a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline + Person:Jennifer Fostel + Pathologist + pathologist role - + - + - + - column chromatography detector - - There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077 - chromatography detector, defined class/xps - column chromatography detector - - - - - - - - - Bruker autosampler - - A Bruker autosampler is an autosampler made by Bruker. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209 - Bruker autosampler - - - - - - - - - organic acid column - - An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 - organic acid column - - - - - - - - - thermal conductivity detector - - The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). - PERSON:Daniel Schober - TCD, hot wire detector - WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084 - thermal conductivity detector - - - - - - - - - Bruker US 2 NMR magnet - - An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189 - NMR instrument - Bruker US 2 NMR magnet - - - - - - - - - protein column + supernatant collection system harvesting frame - A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 - refactor as defined class - protein column + A device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125. + Daniel Schober + google + supernatant collection system harvesting frame - + - - - solvent mixer + + + + + + + + + filter paper - A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 - check on definition ! - solvent mixer - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. - An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. - Philippe Rocca-Serra - Philippe Rocca-Serra - mass spectrometry assay + A device manufacture with the intent to provide a porous unsized paper used for filtering. + Frank Gibson + sep:00107 + filter paper - + - - + + + - - - - - - - - + + + + + + 2 - - study design execution - injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. - - a planned process that carries out a study design - removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. - branch derived - 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. - study design execution - - - - - - - - - Bruker NMR Case sample changer - - The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203 - NMR instrument - Bruker NMR Case sample changer + + + + + + + + + + + + + + + + + + + + cell co-culturing + Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay + + A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. + PlanAndPlannedProcess Branch + OBI branch derived + cell co-culturing - + - - - nano pump system + + + role of Institutional Review Board + An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008 + Animal protocol review board - A pump system optimized for nano flow chromatography. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052 - nano pump system + the role of a organization that is realized by members reviewing study designs for their agreement with regulations + Person:Helen Parkinson + Person:Jennifer Fostel + Internal Review Board + OBI, CDISC + CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial. + role of Institutional Review Board - + - - - Bruker AutoClean system - - NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. - washing system/NMR tube washing system, XPS: device has function washing - PERSON:Daniel Schober - WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 - Bruker AutoClean system + + + eSource document + + an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures + person:Jennifer Fostel + article-without-pmid-or-doi:CDISCglossary + eSource document - + - - - manual injection system - - The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064 - manual injection system + + + crossover population role + + a role realized when a participant serves as reference to itself + Person: Jennifer Fostel + crossover population + crossover population role - + - - - Varian GEMINI spectrometer - - An older Varian Broadband NMR spectrometer. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239 - NMR instrument - Varian GEMINI spectrometer + + + complete nutrient role + Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm + + A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. + Person: Jennifer Fostel + complete nutrient + complete nutrient role - + - - - column connector + + + radiolabel role - A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236 - chromatography device - column connector + a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection + Jennifer Fostel + radiolabel + radiolabel role - - - - - solid NMR probe - - An NMR probe that is designed to hold a solid sample. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243 - NMR device - solid NMR probe - - - + - + + + + + + + + + + + + + + + cDNA library + PMID:6110205. collection of cDNA derived from mouse splenocytes. + + Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. - - - Bruker high resolution probe - - BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. - PERSON:Daniel Schober - HR Probe - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223 - NMR probe - Bruker high resolution probe +ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. + PERSON: Luisa Montecchi + PERSON: Philippe Rocca-Serra + GROUP: PSI + PRS: 22022008. class moved under population, +modification of definition and replacement of biomaterials in previous definition with 'material' +addition of has_role restriction + clonal cDNA library - + - - - chromatography detector + + + electronic case report form - A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012 - chromatography detector + An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11. + person:Jennifer Fostel + CDISC glossary + electronic case report form - + - - - normal phase column + + + placebo role + Pill consisting of inert materials - A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097 - normal phase column + a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance + Person:Jennifer Fostel + placebo + CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product. + placebo role - + - - - APOLLO console - - The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application. - PERSON:Daniel Schober - WEB:<http://www.tecmag.com/apollo.htm> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249 - NMR instrument/NMR console - APOLLO console + + + autotransplantation + + is the transplantation of tissue from one part of \nthe body to another in the same individual. ) + PlanAndPlannedProcess Branch + OBI branch derived + autotransplantation - + - - - NMR sample holder + + + parameter threshold + 0.01, 0.03 - An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212 - NMR device - NMR sample holder + A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role + person:Kevin Clancy + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + parameter threshold - + - - - - - - - - - chromatography instrument - - Any instrument that is used to carry out a chromatography experiment. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262 - chromatography device, defined class? - chromatography instrument + + + study group role + The group of randomized participants that are assigned to a treatment arm of the trial + + a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol + Jennifer Fostel + study group population + study group role - + - - - continuous wave NMR instrument - - Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). - PERSON:Daniel Schober - WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283 - NMR instrument - continuous wave NMR instrument + + + p-value + PMID:19696660 +in contrast to the in-vivo data AT-III increased significantly from +113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2). + + A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. + May be outside the scope of OBI long term, is needed so is retained + PERSON:Chris Stoeckert + WEB: http://en.wikipedia.org/wiki/P-value + p-value - + - - - fourier transformation NMR instrument - - In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. - PERSON:Daniel Schober - GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284 - NMR instrument - fourier transformation NMR instrument + + + population + PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. + + a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: +http://code.google.com/p/popcomm-ontology/ + PERSON: Philippe Rocca-Serra + adapted from Oxford English Dictionnary + rem1: collection somehow always involve a selection process + population - + - - - nitrogen phosphorous detector + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NMR 3D molecular structure determination assay + Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013). - The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089 - nitrogen phosphorous detector + A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. + IEDB + PlanAndPlannedProcess Branch + IEDB + NMR 3D molecular structure determination assay - + - - - cation exchange column - - A cation exchange column is a chromatography column that is used in cation exchange chromatography. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 - cation exchange column + + + + + + + + + imaging assay + + An assay that produces a picture of an entity. + PlanAndPlannedProcess Branch + OBI branch derived + imaging assay - + - - - direct detection NMR probe - - An NMR probe designed to allow the direct detection of acquisition nuclei. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280 - NMR device - direct detection NMR probe + + + protocol optimization objective + + Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol. + Jennifer Fostel + protocol optimization objective - + - - - Bruker B-ACS system - - The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210 - NMR instrument - Bruker B-ACS system + + + role of pathology review board + + a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation + Person: Jennifer Fostel + pathology review board + role of pathology review board - + - + - + - rapid resolution column - - A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102 - rapid resolution column + microtiter plate + A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) + + A microtiter_plate is a flat plate with multiple wells used as small test tubes. + Melanie Courtot + microplate + http://en.wikipedia.org/wiki/Microtiter_plate + microtiter plate - + - - - liquid chromatography autosampler - - Designed to perform capillary LC with injection of sample volumes ranging from nL to L. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061 - liquid chromatography autosampler + + + role of impartial witness + According to GCP , an impartial witness should be present for an +illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html + + a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial + impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who + Person: Helen Parkinson + Person: Jennifer Fostel + impartial witness + role of impartial witness - + - - - vacuum degasser + + + chromatin immunoprecipitation + Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method. - A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/topics/vacuum.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053 - vacuum degasser + An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics. + Bjoern Peters, Randi Vita, James A. Overton + ChIP + OBI + chromatin immunoprecipitation - + - - - capillary column + + + biological replicate role + A member of a dose-time group; a patient in a given arm of a trial - A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066 - capillary column + a reference participant role realized by equivalent treatment of participants + Person:Jennifer Fostel + biological replicate + OBI + biological replicate role - + - - - sample inlet + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + radioactivity detection + Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. - The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head. - PERSON:Daniel Schober - WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044 - chromatography device - sample inlet + An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. + IEDB + PlanAndPlannedProcess Branch + IEDB + radioactivity detection - + - - - NMR tube washing system - - An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204 - NMR instrument - NMR tube washing system - - - - - - - - - NMR console - - A component of an NMR instrument that controls the activities of the other components. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015 - NMR instrument, TODO: same as or part of acquisition computer? - NMR console - - - - - - - - - dual loop autosampler - - A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate). - PERSON:Daniel Schober - WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063 - dual loop autosampler - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - variable wavelength detector - - A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079 - variable wavelength detector - - - - - - - - - Bruker LC-NMR platform - - The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276 - NMR instrument - hyphenated NMR instrument platform - Bruker LC-NMR platform - - - - - - - - - sample injection system - - An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057 - chromatography device - sample injection system + investigation agent role + The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. + + A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. + Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. + Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) + GROUP: Role Branch + investigator + OBI + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + study person role + Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) + investigation agent role - + - - + + - - + + - multiple wavelength detector + nutrient role + Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia. - A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078 - multiple wavelength detector + a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. + GROUP: Role branch + nutrient + Wikipedia, feb 29, 2008 + 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment. + nutrient role - + - - - photoionization detector + + + obsolete_dropout role + Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study) - The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis. - PERSON:Daniel Schober - PID - WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090 - photoionization detector + Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. + Role Branch + OBI + + obsolete_dropout role + true - + - - - gas generator + + + obsolete health care provider role - An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033 - gas chromatography equipment - gas generator + a worker role of providing medical care either within or outside the study timeline + Person:Jennifer Fostel + health care provider + + obsolete health care provider role + true - + - - - column jacket - - A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276 - chromatography device - column jacket + + + methodology testing objective + + Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. + Jennifer Fostel + methodology testing objective - + - - - electron capture detector - - The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes. - PERSON:Daniel Schober - ECD - WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085 - electron capture detector + + + analytical cytology data file + FCS file, ACS file, foo.fcs, foo.asc + + A digital entity intended to capture data in analytical cytology domain. + person:Chris Stoeckert + group:Flow Cytometry community + analytical cytology data file - + - - - reversed phase column + + + proxy respondent role - A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 - reversed phase column + Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel + Jennifer Fostel + proxy respondent + proxy respondent role - + - - - injector lubricant - - A lubricant used in liquid chromatography that eases sample injector penetration. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118 - injector lubricant + + + fluorescence compensation matrix + ((1.053096, -0.22476), (-0.24877, 1.053096)) + + A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix. + person:Chris Stoeckert + group:Flow Cytometry community + fluorescence compensation matrix - + - - - - - - - - - - - - - - + + - - + + - isolation of cell population - removing CD4+ cells from PBMCs using magnetic beads. + negative reference substance role + Saline solution - a process in which a population of cells with certain characteristics is isolated from a larger population - Person: Bjoern Peters - isolation of cell population + a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response + Person: Jennifer Fostel + negative reference substance + negative reference substance role - + - - - DISCOVERY console + + + role of legally acceptable representative + Parent of minor patient; Definition of legally acceptable representative +An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE - The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247 - NMR instrument/NMR console - DISCOVERY console + a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial. + legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary] + Person: Jennifer Fostel + Person:Helen Parkinson + legally acceptable representative + OBI, CDISC + role of legally acceptable representative - + - - - Bruker AMX series NMR instrument - - A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe. - PERSON:Daniel Schober - WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240 - NMR instrument - Bruker AMX series NMR instrument + + + investigation results report + + An investigation report is a report on the results of an investigation. + person:Chris Stoeckert + group:OBI + investigation results report - + - - - chromatofocusing column - - A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. - PERSON:Daniel Schober - WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 - chromatofocusing column + + + cellular feature identification objective + + Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. + Jennifer Fostel + cellular feature identification objective - + - - - - - - - - + + - - + + + + + + + + + - NMR probe + reference subject role + Saline treated rat; one of three identically-treated subjects - Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014 - NMR instrument - NMR probe + a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference + Jennifer Fostel + reference participant + OBI + reference subject role - + - - - NMR magnet + + + vital dye role + typtan blue has a vital dye - A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185 - NMR instrument - NMR magnet + A dye role that is realized when used to detect live cells in an experiment + 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178 + Person: Helen Parkinson + Person: Jennifer Fostel + vital dye + vital dye role - + - - - trap column + + + obsolete_blinded medication role + 115 patients received ipilimumab and blinded medication + Inert pill shaped like aspirin tablet - A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261 - trap column + Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance + Jennifer Fostel + Person:Helen Parkinson + + obsolete_blinded medication role + true - + - - - flow probe + + + sub-investigator role + + a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline + Person: Jennifer Fostel + sub-investigator + CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows + sub-investigator role + + + + + + + + + data encoding + storage of measurement results from an assay into a text file, such as - An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes. - PERSON:Daniel Schober - WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131 - NMR device - flow probe + a documenting process to encode an information entity into a digital document + PlanAndPlannedProcess Branch + OBI branch derived + We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE + data encoding - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - + + + + - Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. - - An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. - Philippe Rocca-Serra - chemical pathology - detection of analyte in blood sample - url:https://en.wikipedia.org/wiki/Clinical_chemistry - clinical chemistry assay + enzymatic cleavage + Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828 + + a material processing that digests the fraction of input material that is susceptible to that enzyme + PlanAndPlannedProcess Branch + OBI branch derived + enzymatic cleavage - + - - - flame ionization detector - - A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. - PERSON:Daniel Schober - FID - WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 - flame ionization detector + + + hardware optimization objective + + Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. + Jennifer Fostel + hardware optimization objective - + - - - vial - - A container made from solid material and primarily used for holding liquid. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Vial - vial + + + obsolete_defined_material + + Place holder class, Utility class to gather the defined classes + Susanna Sansone + OBI Biomaterial derived + + obsolete_defined_material + true - + - - + + - - + + + + + + + + + + + + + + + + + + + + + + - magic angle spinning rotor - - A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle. - PERSON:Daniel Schober - MAS rotor - WEB:<http://www.freepatentsonline.com/4352066.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130 - NMR instrument - magic angle spinning rotor + trial statistician role + + a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. + Person:Jennifer Fostel + trial statistician + CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9] + trial statistician role - + - - - Varian VXR spectrometer - - A Varian NMR spectrometer. - PERSON:Daniel Schober - WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238 - NMR instrument - Varian VXR spectrometer + + + standard error + + A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. + person:Chris Stoeckert + group:OBI + see P-Value + standard error - + - - - splitless GC injector - - Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. - PERSON:Daniel Schober - WEB:<http://en.wikipedia.org/wiki/Gas_chromatography> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060 - splitless GC injector + + + + + + + + + antigen role + + Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response + An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens + Role Branch + OBI + 9Mar09 waiting for discussion with immunology terms + antigen role - + - - - preparative autosampler - - For preparative LC with injection of sample volumes ranging from L to mL ranges. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062 - preparative autosampler + + + software testing objective + + Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. + Jennifer Fostel + software testing objective - + - - - flow high resolution probe + + + sponsor role - Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. - PERSON:Daniel Schober - flow HR-probe - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195 - NMR probe - flow high resolution probe + a responsible party role involved with any of the following activities: initiating, managing and funding a study + Person: Jennifer Fostel + sponsor + CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators + sponsor role - + - - - liquid chromatography valve - - A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110 - chromatography device - liquid chromatography valve - - + + + organization + PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. + + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. + BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers - +2) there are organization_roles (employer, owner, vendor, patent holder) - - - JEOL NMR probe - - An NMR probe that is manufactured by JEOL. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232 - NMR device - JEOL NMR probe - - +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. - +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. - - - Bruker UltraShield Plus NMR magnet - - An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 - NMR instrument - Bruker UltraShield Plus NMR magnet +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now. + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + PERSON: Susanna Sansone + GROUP: OBI + organization - + - - - Bruker CryoProbe + + + feed role + Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008 - The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 - NMR probe - Bruker CryoProbe + a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment. + Person: Jennifer Fostel + feed + OBI + feed role - + - - - column cartridge - - A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 - chromatography device, check on definition ! - column cartridge + + + technical replicate role + Aliquots of a tissue subjected to parallel assays + + technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay + Person: Jennifer Fostel + technical replicate + technical replicate role - + - - - affinity column + + + dye role - An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 - affinity column + A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. + Jennifer Fostel + dye + A substance used to color materials www.answers.com/topic/dye 19feb09 + dye role - + - - - tecmag NMR instrument - - An NMR instrument that is manufactured by tecmag. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 - NMR instrument - tecmag NMR instrument + + + cluster + Cluster of the lymphocytes population. + + A data set which is a subset of data that are a similar to each other in some way. + person:Allyson + person:Chris Stoeckert + group:OBI + cluster - + - - - gel filtration column - - A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 - gel filtration column + + + cohort role + In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008 + + a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study. + Jennifer Fostel + WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students. + WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site). + WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation. + cohort role - + - - - fraction collector - - A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 - fraction collector + + + + + + + + + artificially induced nucleic acid hybridization + www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf + + Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules. + PlanAndPlannedProcess Branch + OBI branch derived + artificially induced nucleic acid hybridization - + - - - - - - - - + + - - - - - - + - Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796 - - An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping - Philippe Rocca-Serra - CNV analysis - copy number variation profiling assay + DNA extraction + + A DNA extraction is a nucleic acid extraction where the desired output material is DNA. + PlanAndPlannedProcess Branch + OBI branch derived + DNA extraction - + - - - in-line filter - - A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity. - PERSON:Daniel Schober - WEB:<http://www.appliedporous.com/frits-chromatography.htm> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123 - in-line filter + + + plan + The plan of researcher X to perform an experiment according to a protocol. + + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. + AR, BP, JM, MC, PRS + branch derived + plan - + - - - imaging NMR probe - - An NMR probe that is designed for generating pictures from sample states via NMR imaging. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244 - NMR device - imaging NMR probe + + + obsolete_sample population + Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 + + A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. + PERSON: Jennifer Fostel + PERSON: Philippe Rocca-Serra + recruited population + GROUP: OBI Biomaterial Branch + + obsolete_sample population + true - + - - - - - - - - - - - - - - - isolation of adherent cells + + + organism feature identification objective - a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. - isolation of adherent cells + Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle. + Jennifer Fostel + organism feature identification objective - + - - - Bruker AC series NMR instrument + + + number of lost events computer + 0, 125, 787 events lost due to computer busy. - A series of older Bruker NMR magnets, now out of production. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241 - NMR instrument - Bruker AC series NMR instrument + A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role + person:Kevin Clancy + Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt + number of lost events computer - + - - - gas chromatography equipment - - Any device used in a gas chromatography experiment. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030 - will become defined class/xps - gas chromatography equipment + + + protocol + PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. + + A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. + PlanAndPlannedProcess Branch + OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) + study protocol + protocol - + - - - syringe filter + + + role of regulator of consumables and medical devices + FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html - A small membrane filter of defined pore size, that filters samples from a syringe. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122 - syringe filter + a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices + Person: Jennifer Fostel + drug regulatoy authority + OBI, CDISC + role of regulator of consumables and medical devices - + - - + + + + + + + + - - + + - Bruker SampleRail system - - This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207 - NMR instrument - Bruker SampleRail system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + adding a material entity into a target + Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. + + is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. + Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. + BP + branch derived + adding a material entity into a target - + - - - column compartment - - For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068 - column compartment + + + + + + + + + + + + + + + + analyte role + Glucose in blood (measured in an assay to determine the concentration of glucose). + + A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. + interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role + pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. + qualities such as weight, color are not assayed but measured, so they do not fall into this category. + GROUP: Role Branch + OBI + Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. + analyte role - + - - - capillary pump system - - A pump system optimized for capillary chromatography. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051 - capillary pump system + + + + + + + + + disease stage + Stage II breast cancer, The timepoint of recovery from a disease + + a part of an occurrence of a disease process which is associated with position in the normal progression of the disease + PERSON: Bjoern peters + disease stage - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - evaporative light scattering detector - - The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082 - evaporative light scattering detector + intraperitoneal injection + + is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe + BP + intraperitoneal injection - + - - + + - - + + + precipitate + Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038 + + a precipitate is a material entity which is output of a precipitation process + PERSON: Philippe Rocca-Serra + precipited material + GROUP: OBI Biomaterial Branch + precipitate + + + + + + + + + protein-protein interaction detection assay + + An assay that determines interactions between proteins, such as protein-protein binding. + protein-protein interaction detection assay + + + + + + + + - + - - + + + + + + + - isolation of PBMCs - cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs. + transcription factor binding site assay + Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. - a process in which cells with a single nucleus are isolated from a blood sample - PERSON: bjoern peters - wiki http://en.wikipedia.org/wiki/PBMC - isolation of PBMCs - - - - - - - - - column cartridger - - A chromatography device where the column cartridge is inserted into and stabilised. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 - check on definition ! - column cartridger + An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors + Philippe Rocca-Serra + TF binding + OBI + https://sourceforge.net/p/obi/obi-terms/767/ + transcription factor binding site assay - + - - - nitrogen generator - - A gas generator that generates nitrogen gas. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034 - nitrogen generator + + + obsolete_enrollment + Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 + + enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules + Bjoern Peters + IEDB + + obsolete_enrollment + true - + - - - needle assembly - - The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 - chromatography device, check on definition ! - needle assembly + + + adverse event trigger + + revisit? + PERSON:Alan Ruttenberg + OBI branch derived + adverse event trigger - + - - + + - + - - + + @@ -11090,250 +16571,264 @@ that has_part some material entity is a material entity. If we add as equivalent - - - - - - - - + + - reverse transcribed polymerase chain reaction - Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. - -Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. -Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. - 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation - Philippe Rocca-Serra - RT-PCR - reverse transcription polymerase chain reaction - reverse transcribed polymerase chain reaction + eluate + Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263 + + a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase + need to add restriction to indicate: has_part some (material entity has_role mobile phase) +need to add mobile phase as role + PERSON: Philippe Rocca-Serra + eluted material + OBI Bionaterial + eluate - + - - - Bruker Capillary LC-NMR platform + + + material to be added role + drug added to a buffer contained in a tube; substance injected into an animal; - Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279 - NMR instrument - hyphenated NMR instrument platform - Bruker Capillary LC-NMR platform + material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process + Role Branch + OBI + 9 March 09 from discussion with PA branch + material to be added role - + - - - gas chromatography oven - - A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039 - gas chromatography equipment - gas chromatography oven + + + obsolete_peritoneum + + is the serous membrane that forms the lining of the abdominal cavity + + obsolete_peritoneum + true - + - - - autosampler - - An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002 - NMR instrument - autosampler + + + + + + + + + + + + + + + interpreting data + Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. + + A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + Bjoern Peters + drawing a conclusion based on data - - - - - isocratic pump system - - A pump system optimized for isocratic chromatography. - PERSON:Daniel Schober - WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049 - isocratic pump system - - - - - - - - - flash pump system - - Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048 - flash pump system - - - - - + - - - Varian UNITY INOVA spectrometer - - The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips. - PERSON:Daniel Schober - WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236 - NMR instrument - Varian UNITY INOVA spectrometer + + + + + + + + + + + + + planning + The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. + + a process of creating or modifying a plan specification + 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. + Bjoern Peters + Bjoern Peters + Plans and Planned Processes Branch + planning - + - - - liquid NMR probe - - An NMR probe that is designed to hold a liquid sample. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242 - NMR device - liquid NMR probe + + + obsolete_documenting + Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. + + Bjoern Peters + wikipedia http://en.wikipedia.org/wiki/Documenting + + + obsolete_documenting + true - + - - - ion exchange column - - An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 - ion exchange column + + + + + + + + + + + + + + + + + + + + + + + + + + + histological sample preparation + + histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay + PERSON:Bjoern Peters + OBI branch derived + histological sample preparation - - - - - Bruker NMR probe - - An NMR probe that is manufactured by Bruker. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231 - NMR device, TODO: May need no definition. - Bruker NMR probe - - + + + + inductive reasoning + Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer. + + a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. + BP: 10/22/122: After changing the parent class to drawing a conclusion *based on data* it is no longer clear that this class is needed; minimally it needs a better definition to distinguish it. - +Proposal is to obsolete. - - - anion trap column - - An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277 - anion trap column + + Bjoern Peters + wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning + inductive reasoning - + - + + + + + + + - fluorescene detector + mass analyzer + The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation - A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080 - fluorescene detector + A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. + Frank Gibson + PERSON: Daniel Schober + http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer + mass analyzer - + - - - tecmag EAGLE probe - - The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248 - NMR probe - tecmag EAGLE probe + + + hypothesis driven investigation + + is an investigation with the goal to test one or more hypothesis + PlanAndPlannedProcess Branch + OBI branch derived + hypothesis driven investigation - + - + + + hypothesis generating investigation + + is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis + PlanAndPlannedProcess Branch + OBI branch derived + hypothesis generating investigation + + + + + + + - + - electrical conductivity detector - - The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239 - electrical conductivity detector + ion source + The ion source of a Voyager-DE??? STR Biospectrometry Workstation + + An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). + Frank Gibson + http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source + ion source - + - + @@ -11341,796 +16836,911 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - NMR instrument - - An Instrument which is used to carry out a NMR analysis of some sample. - PERSON:Daniel Schober - MRI scanner - NMR instrument - magnetic resonance imaging scanner - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 - NMR instrument - NMR instrument - - - - - - - - - Bruker UltraShield NMR magnet - - An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187 - NMR instrument - Bruker UltraShield NMR magnet - - - - - - - - - piston-seal - - The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116 - piston-seal + ion detector + The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation + + An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. + Frank Gibson + http://en.wikipedia.org/wiki/Mass_spectrometry#Detector + ion detector - + - - - mass selective detector + + + + + + + + + metabolite profiling assay + Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 - A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier. - PERSON:Daniel Schober - mass spectrometry detector - WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198 - mass selective detector + An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism + Philippe Rocca-Serra + metabolite assay + metabolomic assay + OBI + metabolite profiling assay - + - - - spin column - - A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 - spin column + + + light emission function + + A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + light emission function - + - - - - - - - - - - - - - - - - - - - - - - manufacturer role - With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. - - Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. - GROUP: Role Branch - OBI - manufacturer role + + + record function + + A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + record function - + - - - transfer line - - A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system. - PERSON:Daniel Schober - WEB:<http://www.freepatentsonline.com/5702671.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235 - chromatography device - transfer line + + + magnify function + + A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + magnify function - + - - - gradient pump system - - A pump system optimized for gradient chromatography. - PERSON:Daniel Schober - WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050 - gradient pump system + + + contain function + A syringe, a beaker + + A contain function is a function to constrain a material entities location in space + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + contain function - + - - - high temperature column - - A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233 - high temperature column + + + heat function + + A heat function is a function that increases the internal kinetic energy of a material + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + heat function - + - - - Bruker Ultrastabilized NMR magnet - - An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188 - NMR instrument - Bruker Ultrastabilized NMR magnet + + + material separation function + + A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + material separation function - + - - + + - - + + - - + + - scattered molecular aggregate - the sodium and chloride ions in a glass of salt water - - a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates - PERSON: Alan Ruttenberg - Collective - Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 - scattered molecular aggregate - - - - - - - - - the phosphate concentration should be 0.1M - - A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. - PERSON: Alan Ruttenberg - Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. - - obsolete_molecular concentration - true - - - - - - - - - - + + - NMR sample tube - - The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132 - NMR device - NMR sample tube - - - - - - - - - Varian UNITY spectrometer - - The predecessor series of the Varian UNITY INOVA spectrometer. - PERSON:Daniel Schober - WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237 - NMR instrument - Varian UNITY spectrometer + ionize process + Electrospray ionization in mass spectrometry + + a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation. + 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize + Person:Bjoern Peters + ionize process - + - - - AVANCE II spectrometer - - A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently. - PERSON:Daniel Schober - WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197 - NMR instrument - AVANCE II spectrometer + + + excitation function + + A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + excitation function - + - - - y-column connector - - A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237 - y-column connector + + + freeze function + + A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + freeze function - + - - - Bruker LC-NMR/MS platform - - Includes the connection to a high-resolution TOF-LC-MS system. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277 - NMR instrument - hyphenated NMR instrument platform - Bruker LC-NMR/MS platform + + + synthesizing function + + A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + synthesizing function - + - - - - - - - - - refractive index detector - - For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081 - refractive index detector + + + perturb function + + A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + http://en.wikipedia.org/wiki/Perturbation_biology + perturb function - + - - - anion exchange column - - An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095 - anion exchange column + + + filter function + + A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through + Frank Gibson + filter function - + - - - plunger column - - A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 - plunger column + + + mechanical function + + A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + http://en.wikipedia.org/wiki/Mechanical_work + mechanical function - + - - - flame photometric detector - - The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected. - PERSON:Daniel Schober - FPD - WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091 - flame photometric detector + + + gas filter function + + A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture + Frank Gibson + gas filter function - + - - - chromatography pump system - - Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). - PERSON:Daniel Schober - WEB:<http://en.wikipedia.org/wiki/Column_chromatography> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046 - chromatography pump system + + + liquid filter function + + A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture + Frank Gibson + liquid filter function - + - - - Bruker 1mm MicroProbe - - Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194 - NMR probe - Bruker 1mm MicroProbe + + + transfer function + + A transfer function is a function to displace a material from one location to another. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + transfer function - + - - - Bruker BEST NMR system - - The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. - PERSON:Daniel Schober - Bruker Efficient Sample Transfer NMR - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206 - NMR instrument - Bruker BEST NMR system + + + electricity supply function + the function of supplying current during a neuroscience experiment. + + An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment. + Daniel Schober + Frank Gibson + Melanie Courtot + power supply + electricity supply function - + - - - chromatography detector filter - - An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121 - chromatography detector filter + + + ionization function + The ion source in amass spectrometer + + An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + http://en.wikipedia.org/wiki/Ionization + ionization function - + - - - cation trap column - - A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278 - cation trap column + + + cool function + + A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. + Daniel Schober + Frank Gibson + Melanie Courtot + cool function - + - - - column adapter - - An Adapter that enabled the connection of a column to additional devices. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113 - chromatography device - column adapter + + + connection function + An electricity cable + + A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + connection function - + - + - + + + + + + + + + + + + + - pulsed amperometric detector + isoelectric focusing device - A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC). - PERSON:Daniel Schober - PAD - WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240 - pulsed amperometric detector + An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated. + Frank Gibson + isoelectric focusing unit + sep:00097 + isoelectric focusing device - - - - - Bruker NMR instrument - - An NMR instrument that is manufactured by Bruker. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198 - NMR instrument - Bruker NMR instrument - - + + + + + + + + + + + + + + + + thermostatic circulator + + A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid + Frank Gibson + sep:00098 + thermostatic circulator + + - - - - Bruker NMR magnet - - An NMR magnet that is manufactured by Bruker. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186 - NMR instrument - Bruker NMR magnet + + + + + energy supply function + + An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy + Frank Gibson + energy supply function - + - - - ozone-induced chemiluminescence detector - - Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry. - PERSON:Daniel Schober - WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088 - ozone-induced chemiluminescence detector + + + + + + + + + + + + + + + information processor function + + An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. + Frank Gibson + data processor function + information processor function - + - - - tecmag NMR console - - An NMR console manufactured by tecmac. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246 - NMR instrument - tecmag NMR console + + + signal conversion function + + A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + transduction function + signal conversion function - + - - - JEOL NMR instrument - - An NMR instrument that is manufactured by JEOL. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226 - NMR instrument - JEOL NMR instrument + + + + + + + + + blot module + + A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised + Frank Gibson + sep:00092 + blot module - + - - - chromatography consumable - - A chromatography consumable is a consumable that is used in a chromatography experiment. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 - chromatography device - chromatography consumable + + + signal amplification function + + A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + signal amplification function - + - - - column frit - - A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density). - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/topics/radial/columns.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070 - chromatography device - column frit + + + + + + + + + + + + + + + image acquisition function + + An image acquisition function is a function to acquire an image of a material + Frank Gibson + image acquisition function - + - - - liquid chromatography column - - A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227 - liquid chromatography column + + + + + + + + + + + + + image acquisition device + + An image creation device is a device which captures a digitized image of an object + Frank Gibson + image acquisition device + sep:00096 + image creation device - + - - - detector lamp - - A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119 - detector lamp + + + solid support function + Taped, glued, pinned, dried or molecularly bonded to a solid support + + A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement + Daniel Schober + Frank Gibson + Melanie Courtot + solid support function - + - - - chart recorder - - The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069 - chromatography device - chart recorder + + + display function + + A display function is a function to present information by translating that information through some lookup process into visual form. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + display function - + - - - open tubular column - - An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. - PERSON:Daniel Schober - WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 - open tubular column + + + environment control function + + An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. + Bill Bug + Daniel Schober + Frank Gibson + Melanie Courtot + environment control function - + - - - high resolution magic angle spin probe - - Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. - PERSON:Daniel Schober - high resolution MAS, hr-MAS - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192 - NMR probe - high resolution magic angle spin probe + + + sort function + + A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. + Daniel Schober + Frank Gibson + Melanie Courtot + sort function - + - - - hydrogen generator + + + + + + + + + + + + + + + gel dryer - A gas generator that generates hydrogen gas. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035 - hydrogen generator + A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels + Frank Gibson + sep:00094 + gel dryer - + - - - glass column - - A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 - glass column + + + + + + + + + primer role + + a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. + (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer + primer role - + - - - auto injector - - A gas chromatography device that can auto-inject a small number of samples an inlet. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058 - auto injector + + + + + + + + + + + + + PCR product + PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. + + is double stranded DNA that is the specified output of a polymerase chain reaction + We are using PCR and not the written out words, as this is the most common used. + GROUP: OBI BIomaterial Branch + GROUP: OBI BIomaterial Branch + PCR product - + - - - Varian NMR instrument - - An NMR instrument that is manufactured by Varian. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234 - NMR instrument - Varian NMR instrument + + + + + + + + + viral RNA extraction + The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703 + + The extraction of RNA from an input material that specifically isolates viral RNA + Person:Bjoern Peters + viral RNA extraction - + - - - Bruker MATCH tube holder system - - The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. - PERSON:Daniel Schober - Bruker Multiple Adjustable Tube Clamp Holder - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211 - NMR instrument - Bruker MATCH tube holder system + + + + + + + + + + + + + + + nucleic acid template role + a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 + + a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. + nucleic acid template role - + - - - Bruker SPE-NMR platform + + + + + + + + + + + + + recombinant plasmid - A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278 - NMR instrument - hyphenated NMR instrument platform - Bruker SPE-NMR platform + a plasmid in which extraneous DNA has been inserted. + PERSON: Bjoern Peters + PERSON: Kevin Clancy + PERSON: Melanie Courtot + GROUP: OBI Biomaterial Branch + recombinant plasmid - + - - - guard column + + + + + + + + + + + + + + + + + cloning vector role + pBluescript plays the role of a cloning vector + + A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning. + JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/ + PERSON: Helen Parkinson + cloning vector role + + + + + + + + + + + + + + + + + + + + + + + + + + + cell cycle synchronization + Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs. - Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111 - chromatography device - guard column + a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle + OBI PA + Bjoern Peters and Nicole Washington + cell cycle synchronization - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + polymerase chain reaction + Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 + + PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. + OBI Plan + PCR + adapted from wikipedai + polymerase chain reaction + + + + + + + + + cloning insert role + + cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process. + Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process" + GROUP: Role branch + OBII and Wikipedia + cloning insert role + + + + + + + + @@ -12142,17 +17752,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - - - + @@ -12163,15 +17763,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - + @@ -12183,180 +17775,137 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203 - - An assay that determines protein expression and translation activity using protein extracts collected from a material entity. - Phlippe Rocca-Serra - proteomic analysis - OBI branch derived - protein expression profiling assay - - - - - - - - - high resolution probe with automatic tuning and matching - - The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. - PERSON:Daniel Schober - High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224 - NMR probe - high resolution probe with automatic tuning and matching + + + + + + + + + + + + + + + + + + + + + + + + + measuring glucose concentration in blood serum assay + Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319. + + An assay that determines the concentration of glucose molecules in a blood serum sample + Bjoern Peters + OBI + measuring glucose concentration in blood serum assay - + - - - fluorine-induced chemiluminescence detector - - A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator. - PERSON:Daniel Schober - WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087 - fluorine-induced chemiluminescence detector + + + + + + + + + + + + + + + + + + reverse transcriptase + + enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase +activity) + person:Melanie Courtot + group:OBI + reverse transcriptase - + - - - size exclusion column - - A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 - size exclusion column + + + obsolete_trypsinized material + A trypsinized suspension of cells + + A material entity that has undergone a process of digestion with trypsin + Person:Bjoern Peters + + obsolete_trypsinized material + true - + - - - chromatography splitter - - An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041 - chromatography device - chromatography splitter + + + + + + + + + syringe + Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 + + A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw + Philippe Rocca-Serra + OBI Instrument adapted from Wikipedia + syringe - + - - - Bruker micro imaging probe - - For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/probes_microimaging.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225 - NMR probe - Bruker micro imaging probe - - - - - - - - - custom made column - - A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234 - custom made column - - - - - - - - - gel permeation column - - A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. - PERSON:Daniel Schober - WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103 - gel permeation column - - - - - - - - - Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 - - An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. - Philippe Rocca-Serra - Nuclear magnetic resonance spectroscopy - url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy - NMR spectroscopy assay - - - - - - - - - Bruker SampleJet system - - Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/automation.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208 - NMR instrument - Bruker SampleJet system - - - - - - - - - JEOL ECX NMR spectrometer + + + + + + + + + extract + Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 - The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. - PERSON:Daniel Schober - WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227 - NMR instrument - JEOL ECX NMR spectrometer + an extract is a material entity which results from an extraction process + PERSON: Philippe Rocca-Serra + extracted material + GROUP: OBI Biomatrial Branch + extract - + - + - + @@ -12364,10 +17913,10 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - - + + @@ -12375,191 +17924,440 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - + - - + + + + + + - + - + - - + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + - Illumina (Solexa) sequencing is an example of DNA sequencing - - A sequencing assay which determines information on the sequence of a DNA molecule. - Philippe Rocca-Serra - nucleotide sequencing - url:https://en.wikipedia.org/wiki/DNA_sequencing - DNA sequencing assay + transcription profiling assay + Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 + + An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. + This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term. + Philippe Rocca-Serra + gene expression profiling + transcription profiling + OBI + transcription profiling assay - + - - - quaternary pump system - - A pump system that pump and mix up to four different solvents in parallel. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047 - quaternary pump system + + + averaging objective + A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. + + An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. + Elisabetta Manduchi + James Malone + PERSON: Elisabetta Manduchi + averaging objective - + - - - carbon nanotube column + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + injection + Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712 - Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. - PERSON:Daniel Schober - WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 - carbon nanotube column + injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. + Philippe Rocca-Serra + OBI Biomaterial + injection - + - - - Bruker solid magic angle spinning probe - - Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. - PERSON:Daniel Schober - solid MAS probe - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193 - NMR probe - Bruker solid magic angle spinning probe + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + enzyme + + (protein or rna) or has_part (protein or rna) and +has_function some GO:0003824 (catalytic activity) + MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything +that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. + person: Melanie Courtot + GROUP:OBI + enzyme - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - + + + + + intraperitoneal administration + Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h + + The administration of a substance into the peritoneum of an organism + Person:Bjoern Peters + intraperitoneal administration + + + + + + + + + + + + + + - - + + - - - + + + + + + + + + + plasmid + + plasmid = DNA and has_quality circular and has_function +(is_realized_as some gene expression) GO:0010467 + person:Melanie Courtot + group:OBI + plasmid + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 + injection into organ section + Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology - An assay that studies blood and blood producing organs using a variety of techniques and instruments - Philippe Rocca-Serra - blood analysis - haematology - OBI branch derived - hematology assay + A process in which an input substance is injected into a organ section. + Person:Bjoern Peters + injection into organ section - + - - - Varian MERCURY spectrometer + + + + + + + + + + + + + + + polyacrylamide gel + Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143 - MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. - PERSON:Daniel Schober - WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235 - NMR instrument - Varian MERCURY spectrometer + a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution + PERSON: Jie Zheng + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch + polyacrylamide gel - + - - - Bruker Metabolic Profiler - - An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. - PERSON:Daniel Schober - WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 - NMR instrument - hyphenated NMR instrument platform - Bruker Metabolic Profiler + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DNA sequence feature detection assay + genotyping using an Affymetrix chip + + An assay with the objective to determine a sequence feature of DNA + Bjoern Peters + Philippe Rocca-Serra + OBI + DNA sequence feature detection assay - + - - - column heater - - The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. - PERSON:Daniel Schober - WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040 - column heater + + + adding material objective + creating a mouse infected with LCM virus + + is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity + BP + adding material objective - + - - + + @@ -12613,1625 +18411,1509 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - - - - + - + - Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 - - An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. - Philippe Rocca-Serra - DNA methylation profiling - OBI branch derived - DNA methylation profiling assay - - - - - - - - - JEOL CapNMR probe + genotyping assay + High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 - The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. - PERSON:Daniel Schober - WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 - NMR probe - JEOL CapNMR probe + An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. + Philippe Rocca-Serra + SNP analysis + genotype profiling + OBI Biomaterial + genotyping assay - + - - + + - + - acquisition computer - - A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 - NMR instrument - acquisition computer - - - - - - - - - gas chromatography detector + needle + Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569 - A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. - PERSON:Daniel Schober - FID - WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 - chromatography detector, defined class/xps - gas chromatography detector + A needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. + Philippe Rocca-Serra + OBI Instrument + needle - + - - - gas purifier - - Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. - PERSON:Daniel Schober - WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036 - gas chromatography equipment - gas purifier + + + analyte measurement objective + The objective to measure the concentration of glucose in a blood sample + + an assay objective to determine the presence or concentration of an analyte in the evaluant + PERSON: Bjoern Peters + PPPB branch + analyte measurement objective - + - - - - - - - - - - - material separation objective - The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. + + + + + + + + + + + + + + + + + + + + + DNA sequence variation detection assay + Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 - is an objective to transform a material entity into spatially separated components. - PPPB branch - PPPB branch - material separation objective - - - - - - - - - indirect detection probe - - An NMR probe designed to allow the indirect detection of acquisition nuclei. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 - NMR device - indirect detection probe + An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. + Philippe Rocca-Serra + OBI Biomaterial + DNA sequence variation detection assay - + - - - JEOL ECA NMR spectrometer + + + + + + + + + agarose gel + Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269 - The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. - PERSON:Daniel Schober - WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx> - http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228 - NMR instrument - JEOL ECA NMR spectrometer + a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch + agarose gel - + - - - atomic emission detector - - Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. - PERSON:Daniel Schober - AED - WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 - atomic emission detector + + + assay objective + the objective to determine the weight of a mouse. + + an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) + PPPB branch + PPPB branch + assay objective - + - - - - - - - - - clustered data set - A clustered data set is the output of a K means clustering data transformation - - A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. - PERSON: James Malone - PERSON: Monnie McGee - data set with assigned discovered class labels - AR thinks could be a data item instead - clustered data set + + + obsolete_heart + Alan Ruttenberg's heart + + The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions + Person:Bjoern Peters + http://en.wikipedia.org/wiki/Heart + + obsolete_heart + true - + - - + + + - - + + - - - data set of features - - A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. - PERSON: James Malone - PERSON: Monnie McGee - data set of features - - - - - - - - + + - + - - - differential expression analysis data transformation + + analyte assay + example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output - A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals. - Dan Berrios - James Malone - Melanie Courtot - Monnie McGee - WEB: - differential expression analysis data transformation + An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. + Alan Ruttenberg + Bjoern Peters + Helen Parkinson + Philippe Rocca-Serra + Alan Ruttenberg + Bjoern Peters + Helen Parkinson + OBI Planned process branch + Philippe Rocca-Serra + analyte assay - + - - - - - - - - + + - - + + - - + + - urine specimen + target of material addition role + peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. - a portion of urine collected from an organism - 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. - This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active - are we happy calling collection of urine a material separation? - urine specimen + target of material addition role is a role realized by an entity into which a material is added in a material addition process + From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. + GROUP: Role Branch + OBI + target of material addition role - + - - - - - - - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - material combination - Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. - - is a material processing with the objective to combine two or more material entities as input into a single material entity as output. - created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. - bp - bp - material combination - - - - - - - - - fuzzy clustering objective - - A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. - James Malone - PERSON: James Malone - PERSON: Ryan Brinkman - fuzzy clustering objective + mass measurement assay + The patients was weighed and mass was determined to be 47 kilograms + + An assay that determines the mass of an evaluant + Helen Parkinson + OBI + mass measurement assay - + - - - - - - - - - device setting - Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification - - a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device - There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133 - PERSON: Frank Gibson - device setting + + + obsolete_identification + DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 + + a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval + Philippe Rocca-Serra + + obsolete_identification + true - + - - - - - - - - + + - - + + - - + + + + + + + - blood specimen - blood drawn from a human for glucose assay - - a material entity derived from a portion of blood collected from an organism - Bjoern Peters - Bjoern Peters - blood specimen + intracellular electrophysiology recording assay + + An electrophysiology assay where the recording location of the electrode is intracellular. + Frank Gibson + Frank Gibson + intracellular electrophysiology recording assay - + - - - - - - - - - data set of predicted values according to fitted curve - - A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. - PERSON: James Malone - PERSON: Monnie McGee - data set of predicted values according to fitted curve + + + packed column + + A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. + PERSON:Daniel Schober + WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218 + packed column - + - - - data representational model - gene regulatory graph model - phylogenetic tree - protein interaction network - - Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. - Melanie Courtot - data structure - data structure specification - GROUP: OBI - 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 - data representational model + + + obsolete_defined_output + example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. + + This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. + PERSON: Alan Ruttenberg + PERSON: James Malone + PERSON: Melanie Courtot + + obsolete_defined_output + true - + - + - + - - + + - - - - - - - - - - - - - drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + regulatory agency + The US Environmental Protection Agency - A planned process with the objective of collecting a specimen. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. - Philly2013: The specimen_role for the specimen is created during the specimen collection process. - label changed to 'specimen collection process' on 10/27/2014, details see tracker: -http://sourceforge.net/p/obi/obi-terms/716/ - Bjoern Peters - specimen collection - 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession - 6/9/09: used at workshop - specimen collection process + A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. + GROUP: OBI Biomaterial Branch + WEB: en.wikipedia.org/wiki/Regulator + regulatory agency - + - + - + - background corrected data set + normalized data set - A data set that is produced as the output of a background correction data transformation. - PERSON: James Malone - PERSON: Melanie Courtot - background corrected data set + A data set that is produced as the output of a normalization data transformation. + PERSON: James Malone + PERSON: Melanie Courtot + normalized data set - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. - An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. - IEDB - ELISA - IEDB - enzyme-linked immunosorbent assay - - - - - - - - - - + + - - - error corrected data set - - A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). - PERSON: James Malone - PERSON: Monnie McGee - error corrected data set - - - - - - - - - - + + + + + - - - - - + - - - - - class prediction data transformation + + + + measure function + A glucometer measures blood glucose concentration, the glucometer has a measure function. - A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. - James Malone - supervised classification data transformation - PERSON: James Malone - class prediction data transformation + Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. + PERSON: Daniel Schober + PERSON: Helen Parkinson + PERSON: Melanie Courtot + PERSON:Frank Gibson + measure function - + - - + + - - - - - - - - - - - - - - - - + + + + + + + + + - - + + - - + + - The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. - A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. - IEDB - IEDB - BrdU incorporation assay - - - - - - - - - Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies + extracellular electrophysiology recording assay + The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron - The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. - IEDB - ICCS - ICS - IEDB - - - intracellular cytokine staining (ICS) - obsolete intracellular cytokine staining assay - true + An electrophysiology assay where the recording location of the electrode is extracellular. + Frank Gibson + Helen Parkinson + Frank Gibson + extracellular electrophysiology recording assay - + - - - - - - - - - - - - - - - - - background correction data transformation + + + + + + + + + consume data function - A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. - James Malone - PERSON: James Malone - background correction data transformation + Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data. + PERSON: Daniel Schober + PERSON: Frank Gibson + PERSON: Melanie Courtot + consume data function - + - - - Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes. - - An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer - IEDB - MHC tetramer assay - IEDB - - - MHC tetramer/multimer staining - obsolete MHC multimer staining assay - true + + + material transformation objective + The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. + + an objective specifiction that creates an specific output object from input materials. + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + artifact creation objective + GROUP: OBI PlanAndPlannedProcess Branch + material transformation objective - + - + - + - - error correction data transformation - - An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. - James Malone - Monnie McGee - EDITORS - error correction data transformation - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - + + + + - - - - - - - - - + + - The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. - A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. - IEDB - IEDB - tritiated thymidine incorporation assay + manufacturing + + Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process + Manufacturing implies reproducibility and responsibility AR + This includes a single scientist making a processed material for personal use. + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + GROUP: OBI PlanAndPlannedProcess Branch + manufacturing - + - - - - - - - - - - - - - - - - + + + manufacturing objective + + is the objective to manufacture a material of a certain function (device) + PERSON: Bjoern Peters + PERSON: Frank Gibson + PERSON: Jennifer Fostel + PERSON: Melanie Courtot + PERSON: Philippe Rocca-Serra + GROUP: OBI PlanAndPlannedProcess Branch + manufacturing objective + + + + + + + + - - + + - sample from organism - - a material obtained from an organism in order to be a representative of the whole - 5/29: This is a helper class for now - we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. - sample from organism + column chromatography detector + + There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077 + chromatography detector, defined class/xps + column chromatography detector - + - - - - - - - - - statistical hypothesis test + + + Bruker autosampler - A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. - James Malone - PERSON: James Malone - statistical hypothesis test + A Bruker autosampler is an autosampler made by Bruker. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209 + Bruker autosampler - + - - - - - - - - - center value - - A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. - PERSON: James Malone - PERSON: Monnie McGee - median - center value + + + organic acid column + + An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 + organic acid column - + - - - statistical hypothesis test objective - - is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation - James Malone - Person:Helen Parkinson - hypothesis test objective - WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing - statistical hypothesis test objective + + + thermal conductivity detector + + The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). + PERSON:Daniel Schober + TCD, hot wire detector + WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084 + thermal conductivity detector - + - - - - - - - - - reduced dimension data set - - A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set. - PERSON: James Malone - PERSON: Monnie McGee - reduced dimension data set + + + Bruker US 2 NMR magnet + + An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189 + NMR instrument + Bruker US 2 NMR magnet - + - - - - portioning objective - The objective to obtain multiple aliquots of an enzyme preparation. - - A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. - portioning objective + + + protein column + + A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 + refactor as defined class + protein column - + - + + + solvent mixer + + A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 + check on definition ! + solvent mixer + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + - - average value - - A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. - PERSON: James Malone - PERSON: Monnie McGee - arithmetic mean - average value + mass spectrometry assay + Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. + + An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. + Philippe Rocca-Serra + Philippe Rocca-Serra + mass spectrometry assay - + - - - + + - + - - + + + + + + + - - - - - - - - - - - - - - whole organism preparation - putting a mouse in the blender. Not: putting a mouse on a scale - - A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained - does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. - whole organism preparation + + + study design execution + injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. + + a planned process that carries out a study design + removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. + branch derived + 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. + + study design execution - + - - - separation into different composition objective - The objective to obtain cells contained in a sample of blood. + + + Bruker NMR Case sample changer - A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). - We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives - separation into different composition objective + The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203 + NMR instrument + Bruker NMR Case sample changer - + - - + + + nano pump system - Study result is an information content entity that is a specified data output of a study. - GROUP: OBI - - obsolete_study result - true + A pump system optimized for nano flow chromatography. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052 + nano pump system - + - - - The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. - - A objective specification to obtain a material entity for potential use as an input during an investigation. - Bjoern Peters - Bjoern Peters - specimen collection objective + + + Bruker AutoClean system + + NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. + washing system/NMR tube washing system, XPS: device has function washing + PERSON:Daniel Schober + WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 + Bruker AutoClean system - + - - - - - - - - - - - - - - - - - - - - - - - - - - - creating a mixture of molecules in solution - The production of PBS + + + manual injection system - is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. - Bjoern Peters - PERSON: Helen Parkinson - creating a mixture of molecules in solution + The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064 + manual injection system - + - - - material combination objective - - is an objective to obtain an output material that contains several input materials. - PPPB branch - bp - material combination objective + + + Varian GEMINI spectrometer + + An older Varian Broadband NMR spectrometer. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239 + NMR instrument + Varian GEMINI spectrometer - + - - - nucleotide overhang cloning - Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs + + + column connector - Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation - Helen Parkinson - nucleotide overhang cloning + A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236 + chromatography device + column connector - + - - - rodent care protocol - Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. - - A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. - Bjoern Peters - Bjoern Peters - rodent care protocol + + + solid NMR probe + + An NMR probe that is designed to hold a solid sample. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243 + NMR device + solid NMR probe - + - - - - - - - - - 454 Genome Sequence 20 - PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. + + + Bruker high resolution probe - is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. - Philippe Rocca-Serra - GS 20 - 454 Genome Sequence 20 + BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. + PERSON:Daniel Schober + HR Probe + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223 + NMR probe + Bruker high resolution probe - + - - - - - - - - + + + chromatography detector + + A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012 + chromatography detector + + + + + + + + + normal phase column + + A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097 + normal phase column + + + + + + + + + APOLLO console + + The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application. + PERSON:Daniel Schober + WEB:<http://www.tecmag.com/apollo.htm> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249 + NMR instrument/NMR console + APOLLO console + + + + + + + + + NMR sample holder + + An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212 + NMR device + NMR sample holder + + + + + + + + - - + + - immunoprecipitation - PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. - - is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity - Philippe Rocca-Serra - OBI plan and planned process branch - immunoprecipitation + chromatography instrument + + Any instrument that is used to carry out a chromatography experiment. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262 + chromatography device, defined class? + chromatography instrument - + - - + + + continuous wave NMR instrument + + Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). + PERSON:Daniel Schober + WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283 + NMR instrument + continuous wave NMR instrument + + + + + + + + + fourier transformation NMR instrument + + In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. + PERSON:Daniel Schober + GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284 + NMR instrument + fourier transformation NMR instrument + + + + + + + + + nitrogen phosphorous detector + + The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089 + nitrogen phosphorous detector + + + + + + + + + cation exchange column + + A cation exchange column is a chromatography column that is used in cation exchange chromatography. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 + cation exchange column + + + + + + + + + direct detection NMR probe + + An NMR probe designed to allow the direct detection of acquisition nuclei. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280 + NMR device + direct detection NMR probe + + + + + + + + + Bruker B-ACS system + + The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210 + NMR instrument + Bruker B-ACS system + + + + + + + + - - + + - ABI 377 automated sequencer + rapid resolution column - is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. - Philippe Rocca-Serra - Applied Biosystems - ABI 377 automated sequencer + A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102 + rapid resolution column - + - - - recombination enzyme based cloning - - a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector - recombination enzyme based cloning + + + liquid chromatography autosampler + + Designed to perform capillary LC with injection of sample volumes ranging from nL to L. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061 + liquid chromatography autosampler - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + vacuum degasser + + A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/topics/vacuum.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053 + vacuum degasser + + + + + + + + + capillary column + + A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066 + capillary column + + + + + + + + + sample inlet + + The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head. + PERSON:Daniel Schober + WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044 + chromatography device + sample inlet + + + + + + + + + NMR tube washing system + + An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204 + NMR instrument + NMR tube washing system + + + + + + + + + NMR console + + A component of an NMR instrument that controls the activities of the other components. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015 + NMR instrument, TODO: same as or part of acquisition computer? + NMR console + + + + + + + + + dual loop autosampler + + A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate). + PERSON:Daniel Schober + WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063 + dual loop autosampler + + + + + + + + - - + + - PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. + variable wavelength detector - A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. - Philippe Rocca-Serra - Methylated DNA immunoprecipitation sequencing assay - url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation - MeDIP-seq assay + A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079 + variable wavelength detector - + - - - - - - - - - - - - - - - - - - - - - animal feeding - giving crickets to a snake. - - animal feeding is a process in which animals are provided with food - In an investigation, this will typically be part of an animal care process - Bjoern Peters - branch derived - animal feeding + + + Bruker LC-NMR platform + + The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276 + NMR instrument + hyphenated NMR instrument platform + Bruker LC-NMR platform - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID: 271968. DNA sequencing with chain-terminating inhibitors. + + + sample injection system - A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position - Philippe Rocca-Serra - Sanger sequencing - dye terminator sequencing - url:https://en.wikipedia.org/wiki/Sanger_sequencing - chain termination sequencing assay + An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057 + chromatography device + sample injection system - + - - + + - - + + - AB SOLiD System - PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. + multiple wavelength detector - is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation - Philippe Rocca-Serra - Applied Biosystems - AB SOLiD System + A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078 + multiple wavelength detector - + - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID: 18388294. Single-molecule DNA sequencing of a viral genome. + + + photoionization detector - A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. - Philippe Rocca-Serra - true single molecule sequencing - url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing - Helicos sequencing assay + The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis. + PERSON:Daniel Schober + PID + WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090 + photoionization detector - + - - - - A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule - Kevin Clancy, Bjoern Peters - ligase - - obsolete_DNA ligase - true + + + gas generator + + An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033 + gas chromatography equipment + gas generator - + - - + + + column jacket + + A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276 + chromatography device + column jacket + + + + + + + + + electron capture detector + + The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes. + PERSON:Daniel Schober + ECD + WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085 + electron capture detector + + + + + + + + + reversed phase column + + A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 + reversed phase column + + + + + + + + + injector lubricant + + A lubricant used in liquid chromatography that eases sample injector penetration. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118 + injector lubricant + + + + + + + + - + - + - - - - - - - + + + isolation of cell population + removing CD4+ cells from PBMCs using magnetic beads. - An assay that measures the occurrence of death events in one or more organisms over time - survival assessment assay + a process in which a population of cells with certain characteristics is isolated from a larger population + Person: Bjoern Peters + isolation of cell population - + - - - - - - - - - support vector machine - - A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. - James Malone - Ryan Brinkman - SVM - PERSON: Ryan Brinkman - support vector machine + + + DISCOVERY console + + The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247 + NMR instrument/NMR console + DISCOVERY console - + - - - - - - - - - - - - - - - - - - - - - - - - self-organizing map - - A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. - James Malone - Ryan Brinkman - SOM - PERSON: Ryan Brinkman - self-organizing map + + + Bruker AMX series NMR instrument + + A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe. + PERSON:Daniel Schober + WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240 + NMR instrument + Bruker AMX series NMR instrument - + - - - - - - - - - 454 Genome Sequencer FLX - PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. + + + chromatofocusing column - is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. - Philippe Rocca-Serra - 454 GS FLX - GS-FLX - adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay - 454 Genome Sequencer FLX + A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind. + PERSON:Daniel Schober + WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 + chromatofocusing column - + - - + + - - + + + + + + + + - Illumina Genome Analyzer II - PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. + NMR probe - is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology - Philippe Rocca-Serra - Illumina Corporation - Illumina Genome Analyzer II + Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014 + NMR instrument + NMR probe - + - - - decision tree induction objective - - A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. - James Malone - decision tree induction objective + + + NMR magnet + + A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185 + NMR instrument + NMR magnet - + - - + + + trap column + + A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261 + trap column + + + + + + + + + flow probe + + An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes. + PERSON:Daniel Schober + WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131 + NMR device + flow probe + + + + + + + + @@ -14240,10 +19922,10 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - - + + @@ -14251,41 +19933,21 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + + + + + + + + + + + - - - - - - - - - - - - - - - - - - Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT. - A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. - IEDB - IEDB - Edman degradation - - - - - - - - @@ -14294,10 +19956,10 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + @@ -14305,503 +19967,289 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - - - - - - - - - - - - - - - PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. + clinical chemistry assay + Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. - A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. - Philippe Rocca-Serra - url:https://en.wikipedia.org/wiki/ABI_Solid_Sequencing - SOLiD sequencing assay + An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. + Philippe Rocca-Serra + chemical pathology + detection of analyte in blood sample + url:https://en.wikipedia.org/wiki/Clinical_chemistry + clinical chemistry assay - + - - - - - - - - - decision tree building data transformation + + + flame ionization detector - A decision tree building data transformation is a data transformation that has objective decision tree induction. - James Malone - PERSON: James Malone - decision tree building data transformation + A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. + PERSON:Daniel Schober + FID + WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 + flame ionization detector - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - laboratory animal care - - a process that realizes an animal care protocol that specifies how animals are kept and maintained - laboratory animal care + + + vial + + A container made from solid material and primarily used for holding liquid. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Vial + vial - + - - + + - - + + - yeast artificial chromosome vector - - a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences - this should be a child of 'chromosome' if we import that from another source - Kevin Clancy, Bjoern Peters - YAC - yeast artificial chromosome vector + magic angle spinning rotor + + A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle. + PERSON:Daniel Schober + MAS rotor + WEB:<http://www.freepatentsonline.com/4352066.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130 + NMR instrument + magic angle spinning rotor - + - - - - - - - - - Li-Cor 4300 DNA Analysis System + + + Varian VXR spectrometer - is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing - Philippe Rocca-Serra - OBI and Li-Cor - Li-Cor 4300 DNA Analysis System + A Varian NMR spectrometer. + PERSON:Daniel Schober + WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238 + NMR instrument + Varian VXR spectrometer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - library preparation - PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. + + + splitless GC injector - is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. - Philippe Rocca-Serra - library construction - library preparation + Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. + PERSON:Daniel Schober + WEB:<http://en.wikipedia.org/wiki/Gas_chromatography> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060 + splitless GC injector - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pathogen challenge - - A pathogen challenge is the administration of a live pathogenic organism to a host - pathogen challenge + + + preparative autosampler + + For preparative LC with injection of sample volumes ranging from L to mL ranges. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062 + preparative autosampler - + - - - GenePattern software + + + flow high resolution probe - a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. - James Malone - Person:Helen Parkinson - WEB: http://www.broadinstitute.org/cancer/software/genepattern/ - GenePattern software + Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. + PERSON:Daniel Schober + flow HR-probe + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195 + NMR probe + flow high resolution probe - + - - - graph of vertices - For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. - - A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. - Bjoern Peters - Chris Stoeckert - James Malone - WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html - graph of vertices + + + liquid chromatography valve + + A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110 + chromatography device + liquid chromatography valve - + - - - animal care protocol - Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. - - An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes - Bjoern Peters - Bjoern Peters - animal care protocol + + + JEOL NMR probe + + An NMR probe that is manufactured by JEOL. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232 + NMR device + JEOL NMR probe - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID: 19275939 - - An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin - Bjoern Peters - Philippe Rocca-Serra - chromatin immunoprecipitation sequencing assay - url:https://en.wikipedia.org/wiki/ChIP-sequencing - ChIP-seq assay + + + Bruker UltraShield Plus NMR magnet + + An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 + NMR instrument + Bruker UltraShield Plus NMR magnet - + - - - - - - - - - HeliScope Single Molecule Sequencer + + + Bruker CryoProbe - is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry - Philippe Rocca-Serra - HeliScope Single Molecule Sequencer + The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 + NMR probe + Bruker CryoProbe - + - - - - - - - - - - - - - - - pathogen role - Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383 + + + column cartridge - pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role - GROUP: Role Branch - OBI - 6 April 2009: from the Vaccine Community - pathogen role + A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 + chromatography device, check on definition ! + column cartridge - + - - - - - - - - - vaccine preparation - The production of B. pertussis vaccine. + + + affinity column - vaccine preparation is a planned process with specified output a vaccine - OBI - vaccine preparation + An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 + affinity column - + - - - - - - - - - immunologic adjuvant role - Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant + + + tecmag NMR instrument - The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. - 11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host. -the role 'adjuvant role' inheres in some 'material entity' and is realized by some 'immune response assay'. - GROUP: Role branch - Vaccine Ontology, Wikipedia, OBI - Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891 - - immunologic adjuvant role + An NMR instrument that is manufactured by tecmag. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 + NMR instrument + tecmag NMR instrument - + - + + + gel filtration column + + A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 + gel filtration column + + + + + + + + + fraction collector + + A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 + fraction collector + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -14810,1166 +20258,1018 @@ the role 'adjuvant role' inheres in some 'material entity' a - + - - - - - - - PMID: 19527607 - - An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. - Philippe Rocca-Serra - NuGO OBI plan branch - glucose tolerance test + copy number variation profiling assay + Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796 + + An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping + Philippe Rocca-Serra + CNV analysis + copy number variation profiling assay - + - - - paired-end library - PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. - - is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs - Philippe Rocca-Serra - mate-paired library - paired-end tag (PET) library - adapted from information provided by Solid web site - paired-end library + + + in-line filter + + A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity. + PERSON:Daniel Schober + WEB:<http://www.appliedporous.com/frits-chromatography.htm> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123 + in-line filter - + - - - - - - - - - ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing). - - A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase - Philippe Rocca-Serra - url:https://en.wikipedia.org/wiki/Sequencing_by_ligation - DNA sequencing by ligation assay + + + imaging NMR probe + + An NMR probe that is designed for generating pictures from sample states via NMR imaging. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244 + NMR device + imaging NMR probe - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - - - - - - - - - + + - PMID: 18987734 + isolation of adherent cells + + a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. + isolation of adherent cells + + + + + + + + + Bruker AC series NMR instrument - A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. - Philippe Rocca-Serra - reversible terminator sequencing - Solexa web site (SS_DNAsequencing.pdf document available on july 2009) - Solexa sequencing assay + A series of older Bruker NMR magnets, now out of production. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241 + NMR instrument + Bruker AC series NMR instrument - + - - - - - - - - - host role - In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 + + + gas chromatography equipment - host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role - 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition - GROUP: Role Branch - 30 Mar09 submitted by vaccine community - OBI - http://en.wikipedia.org/wiki/Host_(biology) - host role + Any device used in a gas chromatography experiment. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030 + will become defined class/xps + gas chromatography equipment - + - - - peak matching - - Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold - James Malone - Ryan Brinkman - PERSON: Ryan Brinkman - peak matching + + + syringe filter + + A small membrane filter of defined pore size, that filters samples from a syringe. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122 + syringe filter - + - - - - - - - - - - - - - - - - + + - - + + - k-nearest neighbors - - A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. - James Malone - k-NN - PERSON: James Malone - k-nearest neighbors + Bruker SampleRail system + + This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207 + NMR instrument + Bruker SampleRail system - + - - - - - - - - - - - + + + column compartment + + For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068 + column compartment + + + + + + + + + capillary pump system + + A pump system optimized for capillary chromatography. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051 + capillary pump system + + + + + + + + + + + + + + + evaporative light scattering detector + + The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082 + evaporative light scattering detector + + + + + + + + + + + + + + + + + + + + + + + + + + + isolation of PBMCs + cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs. + + a process in which cells with a single nucleus are isolated from a blood sample + PERSON: bjoern peters + wiki http://en.wikipedia.org/wiki/PBMC + isolation of PBMCs + + + + + + + + + column cartridger + + A chromatography device where the column cartridge is inserted into and stabilised. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 + check on definition ! + column cartridger + + + + + + + + + nitrogen generator + + A gas generator that generates nitrogen gas. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034 + nitrogen generator + + + + + + + + + needle assembly + + The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 + chromatography device, check on definition ! + needle assembly + + + + + + + + + + + - + - - + + - - - - - - - - - - - - + - + - rodent care - keeping animal + reverse transcribed polymerase chain reaction + Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. + +Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. +Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research. - PPPB branch - PPPB branch - rodent care + reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. + 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation + Philippe Rocca-Serra + RT-PCR + reverse transcription polymerase chain reaction + reverse transcribed polymerase chain reaction - + - - - - - - - - - - - - - cloning plasmid - - A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site. - Note: 'cloning vector role' is really a function. Should be dealt with globally - cloning plasmid + + + Bruker Capillary LC-NMR platform + + Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279 + NMR instrument + hyphenated NMR instrument platform + Bruker Capillary LC-NMR platform - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Pyrosequencing sheds light on DNA sequencing. PMID:1115661 + + + gas chromatography oven - A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. - Philippe Rocca-Serra - url:http://en.wikipedia.org/wiki/Pyrosequencing - pyrosequencing assay + A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039 + gas chromatography equipment + gas chromatography oven - + - - - - - - - - - - - - - - recombinant vector - - A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. - recombinant vector + + + autosampler + + An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002 + NMR instrument + autosampler - + - - - - - - - - - restriction enzyme - The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG - - an enzyme that has a specific target cleavage sites within nucleic acids - Kevin Clancy, Bjoern Peters - 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments - restriction enzyme + + + isocratic pump system + + A pump system optimized for isocratic chromatography. + PERSON:Daniel Schober + WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049 + isocratic pump system - + - - - - - - - - - Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing - - A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. - Philippe Rocca-Serra - url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html - DNA sequencing by synthesis assay + + + flash pump system + + Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048 + flash pump system - + - - - - - - - - + + + Varian UNITY INOVA spectrometer + + The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips. + PERSON:Daniel Schober + WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236 + NMR instrument + Varian UNITY INOVA spectrometer + + + + + + + + + liquid NMR probe + + An NMR probe that is designed to hold a liquid sample. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242 + NMR device + liquid NMR probe + + + + + + + + + ion exchange column + + An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 + ion exchange column + + + + + + + + + Bruker NMR probe + + An NMR probe that is manufactured by Bruker. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231 + NMR device, TODO: May need no definition. + Bruker NMR probe + + + + + + + + + anion trap column + + An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277 + anion trap column + + + + + + + + - - + + - NTP-2000 - - a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents - Jennifer Fostel, Bjoern Peters - NTP-2000 + fluorescene detector + + A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080 + fluorescene detector - + - - - single fragment library - - is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs - Philippe Rocca-Serra - fragment library - single fragment library + + + tecmag EAGLE probe + + The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248 + NMR probe + tecmag EAGLE probe - + - - - - - - - - - - - - + + - - + + - cloning vector - - A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. - cloning vector + electrical conductivity detector + + The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239 + electrical conductivity detector - + - - + + - - + + + NMR instrument + + An Instrument which is used to carry out a NMR analysis of some sample. + PERSON:Daniel Schober + MRI scanner + NMR instrument + magnetic resonance imaging scanner + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 + NMR instrument + NMR instrument + + + + + + + + + Bruker UltraShield NMR magnet + + An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187 + NMR instrument + Bruker UltraShield NMR magnet + + + + + + + + + piston-seal + + The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116 + piston-seal + + + + + + + + + mass selective detector + + A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier. + PERSON:Daniel Schober + mass spectrometry detector + WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198 + mass selective detector + + + + + + + + + spin column + + A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 + spin column + + + + + + + + - + - - - - - - - + + + + - - - - - - - - - - - - + + - restriction enzyme based cloning + manufacturer role + With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. - restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector. - Kevin Clancy, Bjoern Peters - restriction enzyme based cloning + Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. + GROUP: Role Branch + OBI + manufacturer role - + - - - - - - - - - - - - - - - Student's t-test - - Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. - James Malone - WEB: http://en.wikipedia.org/wiki/T-test - Student's t-test + + + transfer line + + A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system. + PERSON:Daniel Schober + WEB:<http://www.freepatentsonline.com/5702671.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235 + chromatography device + transfer line - + - - - material sample role - a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. - - A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. - 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. - - material sample role + + + gradient pump system + + A pump system optimized for gradient chromatography. + PERSON:Daniel Schober + WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050 + gradient pump system - + - - - topologically preserved clustered data set - the output data set generated from a self-organizing map. - - A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. - James Malone - PERSON: James Malone - topologically preserved clustered data set + + + high temperature column + + A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233 + high temperature column - + - - - - - - - - - - - - - - - - - - - - - - - - - - - nucleic acid restriction enzyme digest - - A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site - Kevin Clancy, Bjoern Peters - nucleic acid restriction enzyme digest + + + Bruker Ultrastabilized NMR magnet + + An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188 + NMR instrument + Bruker Ultrastabilized NMR magnet - + - - + + - - + + - - - - - - - + + - Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA. + scattered molecular aggregate + the sodium and chloride ions in a glass of salt water - An assay that determines information about an immune response - Bjoern Peters - Randi Vita - IEDB - immune response assay + a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates + PERSON: Alan Ruttenberg + Collective + Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 + scattered molecular aggregate - + - - - - - - - - - - - - - - - - - material sampling process + + + obsolete_molecular concentration + the phosphate concentration should be 0.1M - A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity - sample collection - sampling - https://github.com/obi-ontology/obi/issues/1002 - material sampling process + A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. + PERSON: Alan Ruttenberg + Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. + + obsolete_molecular concentration + true - + - - - - - - - - - - - - - material sample - blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. - - A material entity that has the material sample role - OBI: workshop - sample population - - sample - material sample + + + + + + + + + NMR sample tube + + The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132 + NMR device + NMR sample tube - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. + + + Varian UNITY spectrometer - A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. - Philippe Rocca-Serra - Sagar Jain - url:https://en.wikipedia.org/wiki/Bisulfite_sequencing - bisulfite sequencing assay + The predecessor series of the Varian UNITY INOVA spectrometer. + PERSON:Daniel Schober + WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237 + NMR instrument + Varian UNITY spectrometer - + - - - - - - - - - CART - - A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. - James Malone - classification and regression trees - BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. - CART + + + AVANCE II spectrometer + + A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently. + PERSON:Daniel Schober + WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197 + NMR instrument + AVANCE II spectrometer - + - - - - - - - - - independent variable specification - In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. - - a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled - 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. - In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - experimental factor - independent variable - Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. - study factor - study design independent variable + + + y-column connector + + A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237 + y-column connector - + - - - - - - - - - dependent variable specification - In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. - - dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. - 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. - In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - dependent variable - WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. - study design dependent variable + + + Bruker LC-NMR/MS platform + + Includes the connection to a high-resolution TOF-LC-MS system. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277 + NMR instrument + hyphenated NMR instrument platform + Bruker LC-NMR/MS platform - + - - + + - - - - - - - - - - - - + + - anticoagulant-containing test tube + refractive index detector - A 'blue top' test tube that contains anticoagulant for storing blood specimens' - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - anticoagulant-containing test tube + For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081 + refractive index detector - + - - - - - - - - - controlled variable specification - In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable. - - Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. - 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid - In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - controlled variable - WEB: http://en.wikipedia.org/wiki/Control_variable - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. - study design controlled variable + + + anion exchange column + + An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095 + anion exchange column - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. - - An assay that measures the amount of antithrombin III in blood. - Alan Ruttenberg - AT-III assay - url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 - human antithrombin-III in blood assay + + + plunger column + + A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 + plunger column - + - - - - - - - - - - - - - - - - - - - - - fluorescently labeled MHC multimer - - A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand - fluorescently labeled MHC multimer + + + flame photometric detector + + The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected. + PERSON:Daniel Schober + FPD + WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091 + flame photometric detector - + - - - survival rate + + + chromatography pump system - A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. - Oliver He - adapted from wikipedia -http://en.wikipedia.org/wiki/Survival_rate - survival rate + Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). + PERSON:Daniel Schober + WEB:<http://en.wikipedia.org/wiki/Column_chromatography> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046 + chromatography pump system - + - - - recombinant BAC cloning - - Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material - http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome - recombinant BAC cloning + + + Bruker 1mm MicroProbe + + Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194 + NMR probe + Bruker 1mm MicroProbe - + - - - multiple testing correction objective - Application of the Bonferroni correction + + + Bruker BEST NMR system - A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously - multiple comparison correction objective - http://en.wikipedia.org/wiki/Multiple_Testing_Correction - multiple testing correction objective + The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. + PERSON:Daniel Schober + Bruker Efficient Sample Transfer NMR + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206 + NMR instrument + Bruker BEST NMR system - + - - - - - - - - - statistical model validation - Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia + + + chromatography detector filter - A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. - Helen Parkinson - http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 - statistical model validation + An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121 + chromatography detector filter - + - - - - - - - - - - - - - - - - - - - - - - - - double blind study execution + + + cation trap column - A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated - Person:Alan Ruttenberg - http://clinicaltrials.gov/ct2/info/glossary#double - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - double blind study execution + A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278 + cation trap column - + - - - transcription factor binding site - - SO:0000235 - PLace_holder for sequence ontology term - transcription factor binding site + + + column adapter + + An Adapter that enabled the connection of a column to additional devices. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113 + chromatography device + column adapter - + - + @@ -15977,588 +21277,321 @@ http://en.wikipedia.org/wiki/Survival_rate - glucometer - Diabetic patients use glucometers to determine their glucose levels - - A measurement device with the function to measure and record the level/amount of glucose in a blood sample - PERSON:Frank Gibson - PERSON:Helen Parkinson - glucose meter - http://en.wikipedia.org/wiki/Glucose_meter - glucometer + pulsed amperometric detector + + A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC). + PERSON:Daniel Schober + PAD + WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240 + pulsed amperometric detector - + - - - purification objective - the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. + + + Bruker NMR instrument - The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest - PERSON:Bjoern Peters - isolation objective - BP - 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality - purification objective + An NMR instrument that is manufactured by Bruker. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198 + NMR instrument + Bruker NMR instrument - + - - - SIINFEKL' is the primary structure of a peptide - The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together - Person:Bjoern Peters - - obsolete_primary structure of protein - true + + + Bruker NMR magnet + + An NMR magnet that is manufactured by Bruker. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186 + NMR instrument + Bruker NMR magnet - + - - - capsule shell + + + ozone-induced chemiluminescence detector - a small rounded gelatinous container - Person:Alan Ruttenberg - http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - capsule shell + Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry. + PERSON:Daniel Schober + WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088 + ozone-induced chemiluminescence detector - + - - - recombinant phage cloning - Insert selection by BamHI methyltransferase protection in P1 phage-based cloning + + + tecmag NMR console - Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro. - Helen Parkinson - http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 - recombinant phage cloning + An NMR console manufactured by tecmac. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246 + NMR instrument + tecmag NMR console - + - - - - - - - - - - - - - - - cross linking - cross linking can be used as a probe to link proteins together, to check protein protein interactions + + + JEOL NMR instrument - A process in which bonds are created that link one polymer to another - PERSON: Chris Stoeckert - http://en.wikipedia.org/wiki/Cross-link - cross linking + An NMR instrument that is manufactured by JEOL. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226 + NMR instrument + JEOL NMR instrument - + - - - spike train datum - Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog + + + chromatography consumable - A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. - needs more work to see exactly what the data set looks like - HP - Helen Parkinson, Alan Ruttenberg - spike train measurement - Jessica Turner, NIF - spike train datum + A chromatography consumable is a consumable that is used in a chromatography experiment. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 + chromatography device + chromatography consumable - + - - - - - - - - - - - - - - - - - - - - PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). + + + column frit - An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. - Alan Ruttenberg - url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 - prothrombin time assay + A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density). + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/topics/radial/columns.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070 + chromatography device + column frit - + - - - - - - - - - - - - - - - - - - - - - - denaturing - Denaturing DNA in alcohol - - Is a process in which the tertiary or secondary structure of a polymer is disrupted - http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 - denaturing - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - informing investigator of subject study arm + + + liquid chromatography column - A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. - 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - informing investigator of subject study arm + A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227 + liquid chromatography column - + - - - - - - - - - - - - - - - - 1 - - - - + + + detector lamp - An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard - AT-III assay - url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 - antithrombin-III berichrome assay + A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119 + detector lamp - - - - - material maintenance objective - - An objective specification maintains some or all of the qualities of a material over time. - PERSON: Bjoern Peters - PERSON: Bjoern Peters - material maintenance objective - - - - - + - - - - - - - - - - - - - - - - - - - presentation of stimulus - The presentation of a flashing light to a monkey during reward training + + + chart recorder - a planned process in which an organism is exposed to some stimulus with the intent to invoke an action - Helen Parkinson, Jessica Turner, Dirk Derom - stimulation of organism - Helen Parkinson, Jessica Turner, Dirk Derom - presentation of stimulus + The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069 + chromatography device + chart recorder - + - - - - - - - - - - - - - - - - - - - - PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). + + + open tubular column - An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. - Alan Ruttenberg - url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 - spectrolyse heparin antifactor-Xa assay - - - - - - - - - - - - - - - - - - - - amplified DNA - Amplied DNA created by PCR - - DNA that has been produced in an enzymatic amplification process - PERSON: Alan Ruttenberg - Alan Ruttenberg - amplified DNA - - - - - - - - - - - - - - - - - - - - - - - - - - informed consent process - - A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. - 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. - Person:Alan Ruttenberg - http://clinicaltrials.gov/ct2/info/glossary#informed - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - informed consent process - - - - - - - - - - - - - - - - - - - - primary structure of DNA macromolecule - - a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. - placeholder for SO - BP et al - primary structure of DNA macromolecule + An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube. + PERSON:Daniel Schober + WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 + open tubular column - + - - - An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus + + + high resolution magic angle spin probe - An assay that measures neural activity in the caudate nucleus - Helen Parkinson - Dirk Derom, OBI - Jessica Turner, NIF - measuring neural activity in the caudate nucleus assay + Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. + PERSON:Daniel Schober + high resolution MAS, hr-MAS + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192 + NMR probe + high resolution magic angle spin probe - + - - - to be treated with active ingredient role - Role of a patient in a group treated with an active substance in a clinical trial - - A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient - Person:Alan Ruttenberg - PERSON: Helen Parkinson - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - to be treated with active ingredient role + + + hydrogen generator + + A gas generator that generates hydrogen gas. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035 + hydrogen generator - + - - - guar gum + + + glass column - Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder. - Helen Parkinson - http://en.wikipedia.org/wiki/Guar_gum - guar gum + A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 + glass column - + - - - Berichrom(r) Antithrombin III (A) Kit + + + auto injector - For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution - Person:Alan Ruttenberg - WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06 - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Berichrom(r) Antithrombin III (A) Kit + A gas chromatography device that can auto-inject a small number of samples an inlet. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058 + auto injector - + - - - - - - - - - micro electrode - A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus + + + Varian NMR instrument - An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system. - Helen Parkinson, Jessica Turner, Dirk Derom - micro electrode measuring device - Jessica Turner, Dirk Derom - micro electrode + An NMR instrument that is manufactured by Varian. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234 + NMR instrument + Varian NMR instrument - + - - - fucoidan + + + Bruker MATCH tube holder system - Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). - Helen Parkinson - http://en.wikipedia.org/wiki/Fucoidan - fucoidan + The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. + PERSON:Daniel Schober + Bruker Multiple Adjustable Tube Clamp Holder + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211 + NMR instrument + Bruker MATCH tube holder system - + - - - - - - - - - - - - - - - calibration - the process of using pH buffer adjust a pH meter - - A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements. - GROUP: OBI Philly workshop - WEB:http://en.wikipedia.org/wiki/calibration - calibration + + + Bruker SPE-NMR platform + + A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278 + NMR instrument + hyphenated NMR instrument platform + Bruker SPE-NMR platform - + - - - - - - - - - - - - - - - - - - - - - - - - - - - anticoagulant tube storage of blood specimen + + + guard column - Storage of a blood specimen in a tube with anticoagulant - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - anticoagulant tube storage of blood specimen + Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111 + chromatography device + guard column - + - + @@ -16573,10 +21606,13 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - + + + + + + + @@ -16590,10 +21626,13 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - + + + + + + + @@ -16606,315 +21645,397 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - - - - - - The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660) + protein expression profiling assay + Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203 - An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. - There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant). - Alan Ruttenberg - OBI call - aPTT assay - url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310 - activated partial thromboplastin time assay + An assay that determines protein expression and translation activity using protein extracts collected from a material entity. + Phlippe Rocca-Serra + proteomic analysis + OBI branch derived + protein expression profiling assay - + - - - - - - - - - filled capsule + + + high resolution probe with automatic tuning and matching - A pill in the form of a small rounded gelatinous container with medicine inside. - Person:Alan Ruttenberg - http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - filled capsule + The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. + PERSON:Daniel Schober + High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224 + NMR probe + high resolution probe with automatic tuning and matching - + - - - - - - - - - - - - - - - - - single blind study execution + + + fluorine-induced chemiluminescence detector - A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated - Person:Alan Ruttenberg - http://clinicaltrials.gov/ct2/info/glossary#single - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - single blind study execution + A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator. + PERSON:Daniel Schober + WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087 + fluorine-induced chemiluminescence detector - + - - - - - - - - - - - - - - - - - - - - PMID:19696660#The thrombin time was determined using thromboclotin assay kit. + + + size exclusion column - An assay that measures the time between the addition of the thrombin and the clot formation in plasma. - Alan Ruttenberg - url:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 - thrombin time assay + A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 + size exclusion column - + - - - recombinant YAC cloning - Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21 - - Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material - Helen Parkinson - http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 - recombinant YAC cloning + + + chromatography splitter + + An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041 + chromatography device + chromatography splitter - + - - - to be treated with placebo role + + + Bruker micro imaging probe - A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - to be treated with placebo role + For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/probes_microimaging.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225 + NMR probe + Bruker micro imaging probe - + - - - - - - - - - treatment portion of study execution + + + custom made column - A planned process, part of a study design execution, during which the treatment of subjects is ongoing - 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - treatment portion of study execution + A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234 + custom made column - + - - - pill + + + gel permeation column - A dose of medicine or placebo in the form of a small pellet. - Person:Alan Ruttenberg - http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - pill + A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. + PERSON:Daniel Schober + WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103 + gel permeation column - + - - - research organization - The SALK institute is a research organization. + + + NMR spectroscopy assay + Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 - An organization formed with a goal to have its members conduct investigations - Person:Bjoern Peters - research organization + An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. + Philippe Rocca-Serra + Nuclear magnetic resonance spectroscopy + url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy + NMR spectroscopy assay - + - - - A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds - Person:Bjoern Peters - - obsolete_primary structure of sequence macromolecule - true + + + Bruker SampleJet system + + Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/automation.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208 + NMR instrument + Bruker SampleJet system - + - - - DNA residue methylation - - a quality of a DNA residue that has a methyl group attached to it - DNA residue methylation + + + JEOL ECX NMR spectrometer + + The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. + PERSON:Daniel Schober + WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227 + NMR instrument + JEOL ECX NMR spectrometer - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + - measurement device - A ruler, a microarray scanner, a Geiger counter. - - A device in which a measure function inheres. - GROUP:OBI Philly workshop - OBI - measurement device + DNA sequencing assay + Illumina (Solexa) sequencing is an example of DNA sequencing + + A sequencing assay which determines information on the sequence of a DNA molecule. + Philippe Rocca-Serra + nucleotide sequencing + url:https://en.wikipedia.org/wiki/DNA_sequencing + DNA sequencing assay - + - - - high molecular weight DNA extract - Extraction of chromosomal DNA from mammalian cells by first isolating nucei - - The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. - PERSON:Chris Stoeckert - OBI - high molecular weight DNA extract + + + quaternary pump system + + A pump system that pump and mix up to four different solvents in parallel. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047 + quaternary pump system - + - - - - - - - - - - - - - - - - - - - manufacturer - - A person or organization that has a manufacturer role - manufacturer + + + carbon nanotube column + + Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well. + PERSON:Daniel Schober + WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 + carbon nanotube column - + - - + + + Bruker solid magic angle spinning probe + + Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. + PERSON:Daniel Schober + solid MAS probe + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193 + NMR probe + Bruker solid magic angle spinning probe + + + + + + + + - - + + + + + + + + + + + + - test tube + hematology assay + Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 + + An assay that studies blood and blood producing organs using a variety of techniques and instruments + Philippe Rocca-Serra + blood analysis + haematology + OBI branch derived + hematology assay + + + + + + + + + Varian MERCURY spectrometer - A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material - Bjoern Peters - collection tube - sample tube - http://en.wikipedia.org/wiki/Test_tube - test tube + MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. + PERSON:Daniel Schober + WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235 + NMR instrument + Varian MERCURY spectrometer - + - - + + + Bruker Metabolic Profiler + + An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. + PERSON:Daniel Schober + WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 + NMR instrument + hyphenated NMR instrument platform + Bruker Metabolic Profiler + + + + + + + + + column heater + + The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. + PERSON:Daniel Schober + WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040 + column heater + + + + + + + + + @@ -16922,681 +22043,534 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + - + - + - - + + - - - - - - - oral ingestion of pill - - An adding a material entity to target with the entity is a pill and the target is the mouth - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - oral ingestion of pill - - - - - - - - - - - - - - - material maintenance - - a process with that achieves the objective to maintain some or all of the characteristics of an input material over time - material maintenance - - - - - - - - + - - + + + + + + + + + + + + - - + + - labeled oligonucleotide - - - a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide - 2010-01-31: Philippe Rocca-Serra -placeholder - Person: Philippe Rocca-Serra - labeled oligonucleotide - - - - - - - - - - - - - - + + + - - + + - - + + - unblinding process - - The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - unblinding process - - - - - - - - - - + + - subject agrees they understand informed consent document - - A process in which a subject receives an informed consent document and agrees that they have understood it - 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - subject agrees they understand informed consent document + DNA methylation profiling assay + Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J._PMID:18218979 + + An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. + Philippe Rocca-Serra + DNA methylation profiling + OBI branch derived + DNA methylation profiling assay - + - - - - - - - - - - - - - - - - - - - - - - informing subject of study arm + + + JEOL CapNMR probe - A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. - 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort - Person:Alan Ruttenberg - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - informing subject of study arm + The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. + PERSON:Daniel Schober + WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 + NMR probe + JEOL CapNMR probe - + - - + + - - - - - - - + - Sysmex CA-6000 Coagulation Analyzer + acquisition computer - The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays - Person:Alan Ruttenberg - web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Sysmex CA-6000 Coagulation Analyzer + A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 + NMR instrument + acquisition computer - + - - - human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660] + + + gas chromatography detector - A medical organization at which sick or injured people are given clinical care - Person:Alan Ruttenberg - Person:Helen Parkinson - modified from the wording of the wordnet definition; http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n - - https://github.com/obi-ontology/obi/issues/1295 - - obsolete hospital - true - - - - - - - - - - - - - - - - - - - - primary structure of RNA molecule - - The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together - Person:Bjoern Peters - primary structure of RNA molecule + A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. + PERSON:Daniel Schober + FID + WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 + chromatography detector, defined class/xps + gas chromatography detector - + - - - test substance role - fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally + + + gas purifier - A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation - Person:Alan Ruttenberg - Group:OBI - test substance role + Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. + PERSON:Daniel Schober + WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036 + gas chromatography equipment + gas purifier - + - - - polyA RNA extraction - - A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - polyA RNA extraction + + + + + + + + + + + material separation objective + The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. + + is an objective to transform a material entity into spatially separated components. + PPPB branch + PPPB branch + material separation objective - + - - - organellar RNA extraction + + + indirect detection probe - A RNA extraction process in which the desired output material is RNA in the organelle(s). - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - organellar RNA extraction + An NMR probe designed to allow the indirect detection of acquisition nuclei. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 + NMR device + indirect detection probe - + - - - - obsolete_diethyl pyrocarbonate - true + + + JEOL ECA NMR spectrometer + + The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. + PERSON:Daniel Schober + WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx> + http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228 + NMR instrument + JEOL ECA NMR spectrometer - + - - - record of missing knowledge - A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. + + + atomic emission detector - a information content entity created to indicate that information about something is not available to the person recording it. - This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. - Bjoern Peters - - record of missing knowledge + Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. + PERSON:Daniel Schober + AED + WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 + atomic emission detector - + - - - - - - - - - - - - - - - - - - - - - - - - - - - Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest. - An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. - IEDB - Philippe Rocca-Serra - IEDB - Philippe Rocca-Serra - western blot assay + + + + + + + + + clustered data set + A clustered data set is the output of a K means clustering data transformation + + A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. + PERSON: James Malone + PERSON: Monnie McGee + data set with assigned discovered class labels + AR thinks could be a data item instead + clustered data set - + - - - total RNA extraction - - A RNA extraction process in which total cellular and organelle RNA are extracted. - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - - total RNA extraction + + + + + + + + + data set of features + + A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. + PERSON: James Malone + PERSON: Monnie McGee + data set of features - + - - - - An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. - - - intracellular staining - obsolete intracellular material detection by flow cytometry assay - true + + + + + + + + + differential expression analysis data transformation + + A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals. + Dan Berrios + James Malone + Melanie Courtot + Monnie McGee + WEB: + differential expression analysis data transformation - + - - + + - - + + + + + + + + + + + + + + - complementary nucleotide probe role - A primer in a PCR reaction. A probe on an Affymetrix chip. + urine specimen - A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence - PERSON:Bjoern Peters - complementary nucleotide probe role + a portion of urine collected from an organism + 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. + This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active + are we happy calling collection of urine a material separation? + urine specimen - + - - + + + + + + + + - - + + - record of unknown sex - A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record. - - a record indicating that the biological sex of an organism is not known. - I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement. - Bjoern Peters - record of unknown sex + + + + + + + material combination + Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. + + is a material processing with the objective to combine two or more material entities as input into a single material entity as output. + created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. + bp + bp + material combination - + - - - cytoplasmic RNA extraction - - A RNA extraction process in which the desired output material is RNA in the cytoplasm. - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - cytoplasmic RNA extraction + + + fuzzy clustering objective + + A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. + James Malone + PERSON: James Malone + PERSON: Ryan Brinkman + fuzzy clustering objective - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay. - - An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. - Philippe Rocca-Serra - Richard Scheuermann - northern blot - northern blot assay - - - - - - - - - Likelihood-ratio test + device setting + Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification - Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models. - Tina Boussard - Likelihood-ratio test + a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device + There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133 + PERSON: Frank Gibson + device setting - + - - + + - + - nuclear RNA extract - Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) - - A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - nuclear RNA extract + + + + + + + + + + + + + blood specimen + blood drawn from a human for glucose assay + + a material entity derived from a portion of blood collected from an organism + Bjoern Peters + Bjoern Peters + blood specimen - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A serum neutralization of viral infectivity assay which is performed in a 96-well plate. - Bjoern Peters - Melanie Courtot - microneutralization assay - 96-well neutralization assay - - - - - + - - - + + - - + + - - establishing cancer cell line - Establishment of HeLa immortal cell line - - is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal - - Helen Parkinson - establishing cancer cell line - - - - - - - - - pattern matching objective - - A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. - Tina Boussard - http://en.wikipedia.org/wiki/Pattern_matching - pattern matching objective + + + data set of predicted values according to fitted curve + + A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. + PERSON: James Malone + PERSON: Monnie McGee + data set of predicted values according to fitted curve - + - - - - - - - - - polyA RNA extract - Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) + + + data representational model + gene regulatory graph model + phylogenetic tree + protein interaction network - A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - polyA RNA extract + Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax. + Melanie Courtot + data structure + data structure specification + GROUP: OBI + 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 + data representational model - + - + - + - - - - - - - + + - - An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. - Philippe Rocca-Serra - RNAO - single-nucleotide-resolution nucleic acid structure mapping assay - - - - - - - - - - + + - + - Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells. - - An assay that quantifies viruses by their hemagglutination activity. - Bjoern Peters - Melanie Courtot - Randi Vita - HA - HI - viral haemagglutinin assay - url:http://en.wikipedia.org/wiki/Hemagglutination_assay - viral hemagglutination assay + specimen collection process + drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation + + A planned process with the objective of collecting a specimen. + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. + Philly2013: The specimen_role for the specimen is created during the specimen collection process. + label changed to 'specimen collection process' on 10/27/2014, details see tracker: +http://sourceforge.net/p/obi/obi-terms/716/ + Bjoern Peters + specimen collection + 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession + 6/9/09: used at workshop + specimen collection process - + - + + + + + + + + + background corrected data set + + A data set that is produced as the output of a background correction data transformation. + PERSON: James Malone + PERSON: Melanie Courtot + background corrected data set + + + + + + + @@ -17606,10 +22580,10 @@ placeholder - + - - + + @@ -17617,21 +22591,76 @@ placeholder - - - - - - - - - - - + + enzyme-linked immunosorbent assay + 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. + + An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. + IEDB + ELISA + IEDB + enzyme-linked immunosorbent assay + + + + + + + + + + + + + + + error corrected data set + + A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for). + PERSON: James Malone + PERSON: Monnie McGee + error corrected data set + + + + + + + + + + + + + + + + + + + + + + + class prediction data transformation + + A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. + James Malone + supervised classification data transformation + PERSON: James Malone + class prediction data transformation + + + + + + + + @@ -17640,10 +22669,10 @@ placeholder - + - + @@ -17651,162 +22680,116 @@ placeholder - + - - - - - - - - - - - + BrdU incorporation assay + The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU. - An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. - Bjoern Peters - Melanie Courtot - influenza neutralization assay - url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/ - serum neutralization of viral infectivity assay + A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. + IEDB + IEDB + BrdU incorporation assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pre-mortem specimen - material obtained through a liver biopsy from a human patient + + + obsolete intracellular cytokine staining assay + Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies - a specimen that was taken from a live organism - Bjoern Peters - MO_705 premortem - pre-mortem specimen + The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. + IEDB + ICCS + ICS + IEDB + + + intracellular cytokine staining (ICS) + obsolete intracellular cytokine staining assay + true - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays. - An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. - IEDB - IEDB - detection of specific nucleic acid polymers with complementary probes + + background correction data transformation + + A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. + James Malone + PERSON: James Malone + background correction data transformation - + - - + + + obsolete MHC multimer staining assay + Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes. + + An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer + IEDB + MHC tetramer assay + IEDB + + + MHC tetramer/multimer staining + obsolete MHC multimer staining assay + true + + + + + + + + + + + + + + + error correction data transformation + + An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. + James Malone + Monnie McGee + EDITORS + error correction data transformation + + + + + + + + @@ -17815,10 +22798,10 @@ placeholder - + - + @@ -17826,7 +22809,7 @@ placeholder - + @@ -17834,323 +22817,444 @@ placeholder - + + + + + + + + - Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody. - An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors. - Bjoern Peters - Melanie Courtot - Randi Vita - HAI - HIA - biological activity - hemagglutination inhibition - viral haemagglutinin inhibition assay - OBI branch derived - viral hemagglutination inhibition assay + tritiated thymidine incorporation assay + The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity. + + A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. + IEDB + IEDB + tritiated thymidine incorporation assay - + - - + + + + + + + + + + + + + + + + - - + + - cytoplasmic RNA extract - Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) - - A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - cytoplasmic RNA extract + sample from organism + + a material obtained from an organism in order to be a representative of the whole + 5/29: This is a helper class for now + we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. + sample from organism - + - - - + + - - + + - - + + + statistical hypothesis test + + A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. + James Malone + PERSON: James Malone + statistical hypothesis test + + + + + + + + - - + + - - cell line immortalization - Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs - - an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line - 4-20-13 MHB: This class was repositioned as a child of 'establishing cell line', based on the existing definition ("the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro"), and examples and other annotations indicating the intent to describe a process through which a new immortal cell line is established from an existing mortal cell line using genetic modification techniques. The definition above was modified to clarify this perspective. - Bjoern Peters - 'establishing immortal cell line through directed genetic modification' - OBI - A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line. - cell line immortalization + + + center value + + A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. + PERSON: James Malone + PERSON: Monnie McGee + median + center value - + - - - random primed DNA labeling - PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. -Methods Mol Biol. 1996;58:27-9. - - a labeling in which random primers are used to uniformly label input DNA - need to add Klenow subunit of DNA polymerase I under material entity - Person: Bjoern Peters -Person: Chris Stoeckert - Person: Philippe Rocca-Serra - PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13. - random primed DNA labeling + + + statistical hypothesis test objective + + is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation + James Malone + Person:Helen Parkinson + hypothesis test objective + WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing + statistical hypothesis test objective - + - - - + + - - - - - - - + - - RNA extract - - an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - Group: UPenn Group - RNA extract + + + reduced dimension data set + + A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set. + PERSON: James Malone + PERSON: Monnie McGee + reduced dimension data set - + - + + + + portioning objective + The objective to obtain multiple aliquots of an enzyme preparation. + + A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. + portioning objective + + + + + + + - - - - - - - - - - - - - - - - - - + + + + - Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - A cytometry assay that monitors a cell population to track how many are killed by other cells. - IEDB - IEDB - cell-cell killing assay + + average value + + A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. + PERSON: James Malone + PERSON: Monnie McGee + arithmetic mean + average value - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - - Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells. - A cell killing assay that measures if and how many target cells are killed within an organism. - IEDB - IEDB - in vivo cell killing assay + + + + + + + + + + + + + + whole organism preparation + putting a mouse in the blender. Not: putting a mouse on a scale + + A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained + does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. + whole organism preparation - + - - - secondary structure of sequence macromolecule - - A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. -Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford. - 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO - Person: Philippe Rocca-Serra - Wikipedia - secondary structure of sequence macromolecule + + + separation into different composition objective + The objective to obtain cells contained in a sample of blood. + + A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). + We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives + separation into different composition objective - + - - - nuclear RNA extraction + + + obsolete_study result - A RNA extraction process in which the desired output material is RNA in the nucleus. - Person: Chris Stoeckert - Person: Jie Zheng - UPenn Group - nuclear RNA extraction + Study result is an information content entity that is a specified data output of a study. + GROUP: OBI + + obsolete_study result + true - + - - + + + specimen collection objective + The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. + + A objective specification to obtain a material entity for potential use as an input during an investigation. + Bjoern Peters + Bjoern Peters + specimen collection objective + + + + + + + + - - + + - survival curve + + + + + + + + + + + + + + + + + + + creating a mixture of molecules in solution + The production of PBS + + is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. + Bjoern Peters + PERSON: Helen Parkinson + creating a mixture of molecules in solution + + + + + + + + + material combination objective - A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://www.graphpad.com/www/book/survive.htm - survival curve + is an objective to obtain an output material that contains several input materials. + PPPB branch + bp + material combination objective - + - - + + + nucleotide overhang cloning + Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs + + Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation + Helen Parkinson + nucleotide overhang cloning + + + + + + + + + rodent care protocol + Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. + + A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. + Bjoern Peters + Bjoern Peters + rodent care protocol + + + + + + + + + + + + + + + 454 Genome Sequence 20 + PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. + + is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. + Philippe Rocca-Serra + GS 20 + 454 Genome Sequence 20 + + + + + + + + + + + + + + + + + + + + + immunoprecipitation + PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. + + is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity + Philippe Rocca-Serra + OBI plan and planned process branch + immunoprecipitation + + + + + + + + + + + + + + + ABI 377 automated sequencer + + is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. + Philippe Rocca-Serra + Applied Biosystems + ABI 377 automated sequencer + + + + + + + + + recombination enzyme based cloning + + a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector + recombination enzyme based cloning + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - + + + + + + + + + + + + + - - Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. - A cytometry assay which measures the degreee to which input cells are replicating. - IEDB - IEDB - cell proliferation assay - - - - - - - - + @@ -18193,10 +23297,15 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - + - - + + + + + + + @@ -18204,7 +23313,20 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - + + + + + + + + + + + + + + @@ -18212,7 +23334,13 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - + + + + + + + @@ -18221,17 +23349,23 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - + + + + + + + - + @@ -18240,274 +23374,149 @@ Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 La - + - PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. - - An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity. - Marcus Chibucos - Philippe Rocca-Serra - Southern blot - OBI - Southern blot assay - - - - - - - - - - + + + MeDIP-seq assay + PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. - An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. - Bjoern Peters - Melanie Courtot - Q-PCR - kinetic polymerase chain reaction - qPCR - quantitative real time polymerase chain reaction - url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction - real time polymerase chain reaction assay + A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. + Philippe Rocca-Serra + Methylated DNA immunoprecipitation sequencing assay + url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation + MeDIP-seq assay - + - - + + - - + + - - + + - protein extract - PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. -J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - - a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, - Person: Philippe Rocca-Serra - OBI & wikipedia - protein extract - - - - - - - - - - + + - total RNA extract - Extraction of total RNA from cells with Qiagen mini RNeasy kit. - - A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - total RNA extract - - - - - - - - - secondary structure of RNA molecule - PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. + animal feeding + giving crickets to a snake. - - 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO - Person: Philippe Rocca-Serra - secondary structure of RNA molecule + animal feeding is a process in which animals are provided with food + In an investigation, this will typically be part of an animal care process + Bjoern Peters + branch derived + animal feeding - + - - - - - - - - - - - - - - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - + + - PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. - - A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe - Philippe Rocca-Serra - RNA ontology - DEPC structure mapping assay + chain termination sequencing assay + PMID: 271968. DNA sequencing with chain-terminating inhibitors. + + A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position + Philippe Rocca-Serra + Sanger sequencing + dye terminator sequencing + url:https://en.wikipedia.org/wiki/Sanger_sequencing + chain termination sequencing assay - + - - + + - - + + - organellar RNA extract - Extraction of organellar RNA from plant cells using organellar RNA binding protein. + AB SOLiD System + PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. - A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - organellar RNA extract + is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation + Philippe Rocca-Serra + Applied Biosystems + AB SOLiD System - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - post mortem specimen - the spleen taken from a dead mouse - - a specimen that was taken from a dead organism - Bjoern Peters - MO_416 postmortem - post mortem specimen - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. - IEDB - IEDB - in vitro cell killing assay - - - - - - - - + + @@ -18516,10 +23525,10 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + - + @@ -18527,161 +23536,194 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + - - - - - - - CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant. - An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. - IEDB - IEDB - reporter cell line analyte detection bioassay + Helicos sequencing assay + PMID: 18388294. Single-molecule DNA sequencing of a viral genome. + + A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. + Philippe Rocca-Serra + true single molecule sequencing + url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing + Helicos sequencing assay - + - - - sequence feature annotation - - Information about a sequence region - Bjoern Peters - Bjoern Peters - place holder for sequence ontology term - sequence feature annotation + + + obsolete_DNA ligase + + A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule + Kevin Clancy, Bjoern Peters + ligase + + obsolete_DNA ligase + true - + - - + + - + - induced hemagglutination - - The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances - MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO. -Dev call Nov 22, 2010: To reflect this, the term's label has been updated to 'induced hemagglutination'. - person: Bjoern Peters - person: Melanie Courtot - hemeagglutination - WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination - induced hemagglutination + + + + + + + + + + + + + + + + + + survival assessment assay + + An assay that measures the occurrence of death events in one or more organisms over time + survival assessment assay - + - - + + - - + + - supplying - Jackson Labs supplies mouse strains. - - The planned process of providing material entities -to be used in an investigation. - Jennifer Fostel - Jennifer Fostel - 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. - supplying + support vector machine + + A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. + James Malone + Ryan Brinkman + SVM + PERSON: Ryan Brinkman + support vector machine - + - - + + - + - - - - - - - + + + + - - + + + self-organizing map + + A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. + James Malone + Ryan Brinkman + SOM + PERSON: Ryan Brinkman + self-organizing map + + + + + + + + - - + + - labeled DNA extract + 454 Genome Sequencer FLX + PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. - a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. - Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. -Added duirng Mar 1, 2010 dev call - Group: OBI group - Group: OBI group - labeled DNA extract + is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. + Philippe Rocca-Serra + 454 GS FLX + GS-FLX + adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay + 454 Genome Sequencer FLX - + - - + + - - + + - cloacal specimen - type of sample used in the PCIRN influenza network + Illumina Genome Analyzer II + PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. - A specimen obtained by inserting a swab deeply into the vent of the cloaca of -an organism and vigorously swabbing the wall. The swab should be deeply -stained with fecal material and is then placed in transport medium. - PERSON: Melanie Courtot - WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf - cloacal specimen + is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology + Philippe Rocca-Serra + Illumina Corporation + Illumina Genome Analyzer II - + - - + + + decision tree induction objective + + A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. + James Malone + decision tree induction objective + + + + + + + + @@ -18693,17 +23735,7 @@ stained with fecal material and is then placed in transport medium. - - - - - - - - - - - + @@ -18711,53 +23743,11 @@ stained with fecal material and is then placed in transport medium. - - - - - - - - - - - + - To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. - An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. - IEDB - IEDB - radio immuno assay - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -18770,27 +23760,26 @@ stained with fecal material and is then placed in transport medium. - + + Edman degradation + Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT. - An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. - Bjoern Peters - Melanie Courtot - RRT-PCR - RT-rt PCR - qRT-PCR - real time reverse-transcription polymerase chain reaction assay + A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. + IEDB + IEDB + Edman degradation - + - - + + @@ -18802,7 +23791,7 @@ stained with fecal material and is then placed in transport medium. - + @@ -18810,272 +23799,309 @@ stained with fecal material and is then placed in transport medium. - + - Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. - A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. - IEDB - IEDB - X-ray crystallography 3D molecular structure determination assay + + + + + + + + + + + + + + + SOLiD sequencing assay + PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. + + A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. + Philippe Rocca-Serra + url:https://en.wikipedia.org/wiki/ABI_Solid_Sequencing + SOLiD sequencing assay - + - - - + + - - + + - - + + + decision tree building data transformation + + A decision tree building data transformation is a data transformation that has objective decision tree induction. + James Malone + PERSON: James Malone + decision tree building data transformation + + + + + + + + - + - - + + + + + + + + + + + + + + + + + + + - A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color. - An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. - IEDB - IEDB - promoter activity detection by reporter gene assay + laboratory animal care + + a process that realizes an animal care protocol that specifies how animals are kept and maintained + laboratory animal care - + - - + + - + + + + yeast artificial chromosome vector + + a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences + this should be a child of 'chromosome' if we import that from another source + Kevin Clancy, Bjoern Peters + YAC + yeast artificial chromosome vector + + + + + + + + + + + + - nasopharyngeal aspirate specimen - type of sample used in the PCIRN influenza network + Li-Cor 4300 DNA Analysis System - A speciemn which derives from nasopharyngeal mucosa after -aspiration. - PERSON: Melanie Courtot - WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf - nasopharyngeal aspirate specimen + is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing + Philippe Rocca-Serra + OBI and Li-Cor + Li-Cor 4300 DNA Analysis System - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - + - freezing storage - a fozen pellet used for later assay + library preparation + PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120. - A storage process in temperature that maintenance the frozen status of the stored entities. - 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" -2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. -Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen. - Person: Alan Ruttenberg, Mathias Brochhausen - MO_481 frozen_storage - OBI - freezing storage + is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors. + Philippe Rocca-Serra + library construction + library preparation - + - - - - - + + + + + + + + + + + + + - + - + - - + + + + + + + + + + + + + + - - + + + + + + + + + + + + - - - - - - - - - - - - - - - Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody. - A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. - IEDB - FACS - IEDB - flow cytometry assay + + + + pathogen challenge + + The administration of a live pathogenic organism to a host. + pathogen challenge - + - - - - - - - - - - - - - - - nasal swab specimen - type of sample used in the PCIRN influenza network + + + GenePattern software - A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of -exudate and epithelial debris for microbiological or cellular examination. - PERSON: Melanie Courtot - WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf - nasal swab specimen + a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. + James Malone + Person:Helen Parkinson + WEB: http://www.broadinstitute.org/cancer/software/genepattern/ + GenePattern software - + - - - - - - - - - - - - - - - - - Dulbecco's modified Eagle medium + + + graph of vertices + For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. - A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. - Logical definition should contain all components listed in textual definition at some point. - PERSON:Bjoern Peters - D-MEM - DMEM - Dulbecco's modified Eagle medium + A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. + Bjoern Peters + Chris Stoeckert + James Malone + WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html + graph of vertices - + - - - - - - - - - animal euthanization - Rats were euthanized with CO2 - - A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject - Helen Parkinson and Melissa Haendel - animal sacrifice - Melissa Haendel - may later be refined with more specific list of organisms - animal euthanization + + + animal care protocol + Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. + + An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes + Bjoern Peters + Bjoern Peters + animal care protocol - + - + - + @@ -19083,10 +24109,10 @@ exudate and epithelial debris for microbiological or cellular examination. - + - + @@ -19094,7 +24120,7 @@ exudate and epithelial debris for microbiological or cellular examination. - + @@ -19103,7 +24129,7 @@ exudate and epithelial debris for microbiological or cellular examination. - + @@ -19112,114 +24138,115 @@ exudate and epithelial debris for microbiological or cellular examination. - Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture. - An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest. - IEDB - Luminex assay - IEDB - cytometric bead array assay + ChIP-seq assay + PMID: 19275939 + + An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin + Bjoern Peters + Philippe Rocca-Serra + chromatin immunoprecipitation sequencing assay + url:https://en.wikipedia.org/wiki/ChIP-sequencing + ChIP-seq assay - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + + + HeliScope Single Molecule Sequencer + + is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry + Philippe Rocca-Serra + HeliScope Single Molecule Sequencer + + + + + + + + + + + + + - - + + - labeled RNA extract + pathogen role + Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383 - a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. - Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. -Added duirng Mar 1, 2010 dev call - Group: OBI group - Group: OBI group - labeled RNA extract + pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role + GROUP: Role Branch + OBI + 6 April 2009: from the Vaccine Community + pathogen role - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - frozen specimen - Frozen blood plasma - - A specimen that has been frozen in order to store it. - Person:Alan Ruttenberg - MO_610 frozen_sample - frozen specimen + + + + + + + + + vaccine preparation + The production of B. pertussis vaccine. + + vaccine preparation is a planned process with specified output a vaccine + OBI + vaccine preparation - + - - + + + + + + + + + immunologic adjuvant role + Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant + + The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. + 11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host. +the role 'adjuvant role' inheres in some 'material entity' and is realized by some 'immune response assay'. + GROUP: Role branch + Vaccine Ontology, Wikipedia, OBI + Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891 + + immunologic adjuvant role + + + + + + + + @@ -19228,10 +24255,10 @@ Added duirng Mar 1, 2010 dev call - + - - + + @@ -19239,263 +24266,323 @@ Added duirng Mar 1, 2010 dev call - + + + + + + + + + + + - Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow. - A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. - IEDB - IEDB - surface plasmon resonance binding assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + glucose tolerance test + PMID: 19527607 + + An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. + Philippe Rocca-Serra + NuGO OBI plan branch + glucose tolerance test - + - - - - - - - - - - - - - - - - - labeled specimen + + + paired-end library + PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. - A specimen that has been modified in order to be able to detect it in future experiments - added during call 3/1/2010 - OBI group - labeled specimen + is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs + Philippe Rocca-Serra + mate-paired library + paired-end tag (PET) library + adapted from information provided by Solid web site + paired-end library - + - - + + + - - + + - - - infectious agent + + DNA sequencing by ligation assay + ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing). - is a material entity bearing the disposition to infect an organism - IEDB - IEDB - infectious agent - - - - - - - - - - obsolete_ambidexterious handedness - true + A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase + Philippe Rocca-Serra + url:https://en.wikipedia.org/wiki/Sequencing_by_ligation + DNA sequencing by ligation assay - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + - lyophilization storage - - - a storage process with input material entity and output freeze dried material for long time storage - PERSON: Chris Stoeckert - PERSON: Jie Zheng - - can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed - lyophilization storage + Solexa sequencing assay + PMID: 18987734 + + A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. + Philippe Rocca-Serra + reversible terminator sequencing + Solexa web site (SS_DNAsequencing.pdf document available on july 2009) + Solexa sequencing assay - + - - - material combination function - A stirrer has a material combination function + + + + + + + + + host role + In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 - A material separation function is a function that decreases the resolution between two or more material entities. - Helen Parkinson - OBI - material combination function + host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role + 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition + GROUP: Role Branch + 30 Mar09 submitted by vaccine community + OBI + http://en.wikipedia.org/wiki/Host_(biology) + host role - + - - - EBI provides training on databases and tools and has a training service provider role + + + peak matching - a service provider role which is realized by a servicer provider organization performing some training - PERSON:Helen Parkinson - OBI - - obsolete_training service provider role - true + Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold + James Malone + Ryan Brinkman + PERSON: Ryan Brinkman + peak matching - + - - + + + + + + + + + + + + + + + + - - + + - calorimeter - - A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. - PERSON:Bjoern Peters - calorimetry instrument? - http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm - calorimeter + k-nearest neighbors + + A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. + James Malone + k-NN + PERSON: James Malone + k-nearest neighbors - + - - + + - - - - - - - - - - - - + + + + - + - + - - - - - - - + + - study intervention - - the part of the execution of an intervention design study which is varied between two or more subjects in the study - PERSON: Bjoern Peters - GROUP: OBI - study intervention + + + + + + + + + + + + + + + + + + + + + + + + rodent care + keeping animal + + rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research. + PPPB branch + PPPB branch + rodent care - + - + - + - - + + - material separation device - flow cytometer + cloning plasmid - A device with a separation function realized in a planed process - material separation device + A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site. + Note: 'cloning vector role' is really a function. Should be dealt with globally + cloning plasmid - + - - + + - - - - - - positron emission tomography scanner - - A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. - PERSON:Bjoern Peters - PET scanner? - http://en.wikipedia.org/wiki/Positron_emission_tomography - positron emission tomography scanner - - - - - - - - - - - - @@ -19504,250 +24591,196 @@ Added duirng Mar 1, 2010 dev call - + + + + + + + + - + - - - - - - - - - + + + + + + - - - - - - - - - intramuscular injection - - is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe - intramuscular injection - - - - - - - - - - - - - - micromanipulator + pyrosequencing assay + Pyrosequencing sheds light on DNA sequencing. PMID:1115661 - A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. - PERSON:Bjoern Peters - http://en.wikipedia.org/wiki/Micromanipulator - micromanipulator + A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. + Philippe Rocca-Serra + url:http://en.wikipedia.org/wiki/Pyrosequencing + pyrosequencing assay - + - - - A person or organization who provides access to a DNA sequencer. + + + + + + + + + + + + + + recombinant vector - a service provider role which is realized by a servicer provider organization performing access to some material - PERSON:Helen Parkinson - OBI - - obsolete_material access provider role - true + A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. + recombinant vector - - - - - - obsolete_left handedness - true - - - - - + - - + + - - + + - categorical measurement datum - - A measurement datum that is reported on a categorical scale - Bjoern Peters - nominal mesurement datum - Bjoern Peters - - categorical measurement datum + restriction enzyme + The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG + + an enzyme that has a specific target cleavage sites within nucleic acids + Kevin Clancy, Bjoern Peters + 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments + restriction enzyme - + - - + + + - - + + - - - training process - e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility + + DNA sequencing by synthesis assay + Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing - a process that achieves a training objective - training process + A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. + Philippe Rocca-Serra + url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html + DNA sequencing by synthesis assay - + - - - optical microscope - - A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range - PERSON:Bjoern Peters - optical microscope + + + + + + + + + + + + + + + NTP-2000 + + a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents + Jennifer Fostel, Bjoern Peters + NTP-2000 - + - - - - - - - - - - - - - - - - service consumer role - A biologist who uses a sequencing services fulfills the role of a service consumer - - a role which inheres in a person who uses a service - Person:Helen Parkinson - OBI - service consumer role + + + single fragment library + + is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs + Philippe Rocca-Serra + fragment library + single fragment library - + - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - + + - intradermal injection + cloning vector - is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - intradermal injection + A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. + cloning vector - + - - + + - - + + - + - + - - + + @@ -19756,313 +24789,218 @@ Added duirng Mar 1, 2010 dev call - - - - - chemical cleavage - PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. -Biochimie. 2010 Feb 18. - - chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent - PERSON:Philippe Rocca-Serra - RNA ontology group - chemical cleavage - - - - - - - - - - - - - - - - - + - - - - + + + + + + + + + - The Edinburgh handedness assay is a specific method of determing handedness - - An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. - Helen Parkinson - handedness test - url:http://en.wikipedia.org/wiki/Handedness - handedness assay - - - - - - - - - - - - - - - vibration isolation table - - A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor. - PERSON:Bjoern Peters - United States Patent 6877711 - vibration isolation table - - - - - - - - - sterilization function + restriction enzyme based cloning - a function to remove viable organisms from an input material - sterilization function + restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector. + Kevin Clancy, Bjoern Peters + restriction enzyme based cloning - + - - + + - - - - - - - - - + + - - + + - service provider role - Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. + Student's t-test - is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person - PERSON:Helen Parkinson - service provider role + Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. + James Malone + WEB: http://en.wikipedia.org/wiki/T-test + Student's t-test - + - - - - - - - - - oscilloscope - - A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis). - PERSON:Bjoern Peters - http://en.wikipedia.org/wiki/Oscilloscope - oscilloscope + + + material sample role + a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. + + A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. + 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. + + material sample role - + - - - accessed material role - the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism - - is realized in a planned process where the bearer participates - AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it - accessed material role + + + topologically preserved clustered data set + the output data set generated from a self-organizing map. + + A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. + James Malone + PERSON: James Malone + topologically preserved clustered data set - + - + + - + - - - - - - + + + + + - - - - - - - - - paraffin specimen - liver tissue embedded in paraffin + nucleic acid restriction enzyme digest - a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_990 paraffin_sample - paraffin specimen + A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site + Kevin Clancy, Bjoern Peters + nucleic acid restriction enzyme digest - + - - + + - + + + + + + + - - - - - - - - - - - - - - - - + + + + - compound treatment design - - an intervention design in which the treatment is the administration of a compound - This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. - PERSON: Bjoern Peters - MO_555 compound_treatment_design - compound treatment design + immune response assay + Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA. + + An assay that determines information about an immune response + Bjoern Peters + Randi Vita + IEDB + immune response assay - + - + - + - - - - - - - - - - - - + + + + + + - - - - - - - - oral administration + material sampling process - An administering substance in vivo into the mouth of an organism - PERSON: Melanie Courtot - oral administration + A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity + sample collection + sampling + https://github.com/obi-ontology/obi/issues/1002 + material sampling process - + - + - - + + + + + - processed specimen - A tissue sample that has been sliced and stained for a histology study. -A blood specimen that has been centrifuged to obtain the white blood cells. - - A specimen that has been intentionally physically modified. - Bjoern Peters - Bjoern Peters - A tissue sample that has been sliced and stained for a histology study. - processed specimen + material sample + blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. + + A material entity that has the material sample role + OBI: workshop + sample population + + sample + material sample - + - - + + + - - - - @@ -20071,21 +25009,45 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - + + + + + + + + + + + - + - + + + + + + + + + + + + + + + @@ -20093,63 +25055,37 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - + - - + + + + + + + + + - subcutaneous injection - - is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - subcutaneous injection - - - - - - - - - - + + - electrode puller - - A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube. - PERSON:Bjoern Peters - http://faculty.plattsburgh.edu/donald.slish/Puller1.html - electrode puller - - - - - - - - - - - obsolete_handedness - true - - - - - - - - - + + + + + + + + @@ -20158,138 +25094,188 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - + - - An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. - self reported handedness assessment - - - - - - - - - - - - - - - - - - - - - + + - vibrotome - - A preparation device that uses a vibrating razor blade to cut through tissue. - vibrotome + bisulfite sequencing assay + PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. + + A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. + Philippe Rocca-Serra + Sagar Jain + url:https://en.wikipedia.org/wiki/Bisulfite_sequencing + bisulfite sequencing assay - + - - - reagent application function - An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. - - A function that is realized when a reagent is automatically added to some research material. - PERSON: Nicole Vasilevsky, Matthew Brush - PERSON: Nicole Vasilevsky, Matthew Brush - 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people? - reagent application function + + + + + + + + + CART + + A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. + James Malone + classification and regression trees + BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. + CART - + - - - addition of molecular tracer function - Immunohistochemical labeling of tissue sections by an autostainer staining system. - - A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. - PERSON: Nicole Vasilevsky, Matthew Brush - PERSON: Nicole Vasilevsky, Matthew Brush - addition of molecular tracer function + + + + + + + + + independent variable specification + In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. + + a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled + 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. + In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert + experimental factor + independent variable + Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + study factor + study design independent variable - + - - - training objective - A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package - - An objective specification which is fulfilled by the provision of some training. - Helen Parkinson - OBI - training objective + + + + + + + + + dependent variable specification + In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. + + dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. + 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. + In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert + dependent variable + WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + study design dependent variable - + - - - categorical label - The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. + + + + + + + + + + + + + + + + + + + anticoagulant-containing test tube - A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. - Bjoern Peters - Bjoern Peters - categorical label + A 'blue top' test tube that contains anticoagulant for storing blood specimens' + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + anticoagulant-containing test tube - + - - - - An assay in which a measurement is made by observing entities located in a live cell. - in live cell assay + + + + + + + + + controlled variable specification + In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable. + + Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. + 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid + In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert + controlled variable + WEB: http://en.wikipedia.org/wiki/Control_variable + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. + study design controlled variable - + - - + + + - + - + - + - - - - + + + + + + + + + @@ -20297,335 +25283,372 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - + + + + + + + + + + + + - - - - - lyophilized specimen - freezing dried DNA - - a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_589 freeze_dried_sample - lyophilized specimen - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - + + - Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. - - An assay in which a measurement is made by observing entities located in an organism. - Bjoern Peters - in vivo assay - in live organism assay - - - - - - - - - - - + + + + - - + + - - - - container - - A device that can be used to restrict the location of material entities over time - 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) - PERSON: Bjoern Peters - container + + + + human antithrombin-III in blood assay + PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. + + An assay that measures the amount of antithrombin III in blood. + Alan Ruttenberg + AT-III assay + url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 + human antithrombin-III in blood assay - + - - + + + + + + + + - + - - + + - - - - - - - - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + fluorescently labeled MHC multimer + + A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand + fluorescently labeled MHC multimer + + -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. + -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. + + + survival rate + + A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. + Oliver He + adapted from wikipedia +http://en.wikipedia.org/wiki/Survival_rate + survival rate + + -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device + + + + + recombinant BAC cloning + + Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material + http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome + recombinant BAC cloning - + - - - dose specification - a protocol specifying to administer 1 ml of vaccine to a mouse - - a directive information entity that describes the dose that will be administered to a target - dose specification + + + multiple testing correction objective + Application of the Bonferroni correction + + A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously + multiple comparison correction objective + http://en.wikipedia.org/wiki/Multiple_Testing_Correction + multiple testing correction objective - + - - - - - - - - - + + - - 1 + + - - scalar score from composite inputs + + + statistical model validation + Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia - A measurement datum which is the result of combining multiple datum. For example, a mean or summary score. - JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question. - Person: Jessica Turner - questionaire score - Person: Jessica Turner - JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation? - scalar score from composite inputs + A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. + Helen Parkinson + http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 + statistical model validation - + - - - - fresh specimen - a liver freshly removed from a rat - - a specimen that is output of a specimen creation process used for an investigation without storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_730 fresh_sample - fresh specimen + + + + + + + + + + + + + + + + + + + + + + + + double blind study execution + + A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated + Person:Alan Ruttenberg + http://clinicaltrials.gov/ct2/info/glossary#double + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + double blind study execution - + - + - a processed material created to have a function and which requires electrical power to execute - - obsolete_electrically powered device + obsolete transcription factor binding site + + SO:0000235 + + PLace_holder for sequence ontology term + https://github.com/obi-ontology/obi/issues/1553 + + obsolete transcription factor binding site true - + - + + - - - - - - - - - + + + + - sequence data - example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. + glucometer + Diabetic patients use glucometers to determine their glucose levels + + A measurement device with the function to measure and record the level/amount of glucose in a blood sample + PERSON:Frank Gibson + PERSON:Helen Parkinson + glucose meter + http://en.wikipedia.org/wiki/Glucose_meter + glucometer + + + + + + + + + purification objective + the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. - - Person:Chris Stoeckert - GROUP: OBI - sequence data + The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest + PERSON:Bjoern Peters + isolation objective + BP + 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality + purification objective - + - + + obsolete_primary structure of protein + SIINFEKL' is the primary structure of a peptide + + The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together + Person:Bjoern Peters - obsolete_right handedness + obsolete_primary structure of protein true - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. - A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. - IEDB - IEDB - cell-cell binding detection by flow cytometry assay + + + capsule shell + + a small rounded gelatinous container + Person:Alan Ruttenberg + http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + capsule shell - + - - + + + recombinant phage cloning + Insert selection by BamHI methyltransferase protection in P1 phage-based cloning + + Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro. + Helen Parkinson + http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 + recombinant phage cloning + + + + + + + + - - + + - + + + + + cross linking + cross linking can be used as a probe to link proteins together, to check protein protein interactions + + A process in which bonds are created that link one polymer to another + PERSON: Chris Stoeckert + http://en.wikipedia.org/wiki/Cross-link + cross linking + + + + + + + + + spike train datum + Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog + + A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. + needs more work to see exactly what the data set looks like - HP + Helen Parkinson, Alan Ruttenberg + spike train measurement + Jessica Turner, NIF + spike train datum + + + + + + + + + + + + + + + + + - - - - - - - + + + + - handedness categorical measurement datum - - A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally - PERSON:Alan Ruttenberg - PERSON:Jessica Turner - handedness categorical measurement datum + prothrombin time assay + PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). + + An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. + Alan Ruttenberg + url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 + prothrombin time assay - + - - + + - - + + @@ -20634,500 +25657,423 @@ In the examples above, a reagent is an operational component of a device, but th - + - paraffin storage - - - a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - need to specify paraffin or wax is one of specified input of the process - paraffin storage - - - - - - - - + denaturing + Denaturing DNA in alcohol - An assay in which a measurement is made by observing entities located in a container. - in container assay + Is a process in which the tertiary or secondary structure of a polymer is disrupted + http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 + denaturing - + - - - DNA sequencing of a sample by a core lab which returns data to the consumer - - a service provider role which is realized by a servicer provider organization performing a protocol execution - PERSON:Helen Parkinson - - obsolete_protocol service provider role - true - - - - - - - - - - - - - - + + + + + + + + - + - - + + - - - - - - - agar stab specimen - - a specimen that is output of a process that cell culture inoculated into agar for long term storage. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - MO_971 agar_stab - agar stab specimen - - - - - - - - - - - - - + + + + + + + + + + + + + - computed tomography scanner + informing investigator of subject study arm - An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation. - PERSON:Bjoern Peters - CT scanner - X-ray computed tomography scanner - http://en.wikipedia.org/wiki/X-ray_computed_tomography - computed tomography scanner + A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + informing investigator of subject study arm - + - - + + + - - + + - - - - - - - - - - - - + + + + + + 1 - - - - - - - - intranasal mucosal administration - - The administration of a substance into the intranasal mucosis of an organism - PERSON: Melanie Courtot - intranasal mucosal administration + antithrombin-III berichrome assay + + An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard + AT-III assay + url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 + antithrombin-III berichrome assay - + - - - dose - An organism has been injected 1ml of vaccine - - A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. - dose + + + material maintenance objective + + An objective specification maintains some or all of the qualities of a material over time. + PERSON: Bjoern Peters + PERSON: Bjoern Peters + material maintenance objective - + - - - - - - - - - - - - - - - - - - + + - + - + - - + + - growth condition intervention design + presentation of stimulus + The presentation of a flashing light to a monkey during reward training - A study design in which the independent variable is the environmental condition in which the specimen is growing - PERSON: Bjoern Peters - MO_588 growth_condition_design - growth condition intervention design - - - - - - - - - - A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments - - obsolete_DNA sequencing training service - true - - - - - - - - - - - obsolete_general scalar measurement datum - true - - - - - - - - - Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache. - - The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis - - https://github.com/obi-ontology/obi/issues/623 - obsolete performing a diagnosis - true + a planned process in which an organism is exposed to some stimulus with the intent to invoke an action + Helen Parkinson, Jessica Turner, Dirk Derom + stimulation of organism + Helen Parkinson, Jessica Turner, Dirk Derom + presentation of stimulus - + - - + + - + + + + + + + - - + + - PCR instrument - - A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. - 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. - PCR instrument + spectrolyse heparin antifactor-Xa assay + PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). + + An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. + Alan Ruttenberg + url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 + spectrolyse heparin antifactor-Xa assay - + - - - electron microscope - - A microscope that produces an image of an object by targeting it with an electron beam - electron microscope + + + + + + + + + + + + + + amplified DNA + Amplied DNA created by PCR + + DNA that has been produced in an enzymatic amplification process + PERSON: Alan Ruttenberg + Alan Ruttenberg + amplified DNA - + - - + + - - + + - - 1 + + + + + + + - Edinburgh score - - A score that measures the dominance of a person's right or left hand in everyday activities. - Person: Alan Ruttenberg - Person:Jessica Turner - PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 - WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html - Edinburgh score + informed consent process + + A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate. + 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. + Person:Alan Ruttenberg + http://clinicaltrials.gov/ct2/info/glossary#informed + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + informed consent process - + - + - - - + + + - - + + - - - - - - - - - - - - - + - - DNA sequencing service + + + primary structure of DNA macromolecule - A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. - Eagle-i will supply better English definition - DNA sequencing service + a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. + placeholder for SO + BP et al + primary structure of DNA macromolecule - + - - - service provision objective - A sequencing centre has a service provision objective + + + measuring neural activity in the caudate nucleus assay + An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus - An objective which is fulfilled by the provision of some service e.g. a training service - Helen Parkinson - OBI - service provision objective + An assay that measures neural activity in the caudate nucleus + Helen Parkinson + Dirk Derom, OBI + Jessica Turner, NIF + measuring neural activity in the caudate nucleus assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - intravenous injection - - is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe - PERSON: Melanie Courtot - intravenous injection + + + to be treated with active ingredient role + Role of a patient in a group treated with an active substance in a clinical trial + + A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient + Person:Alan Ruttenberg + PERSON: Helen Parkinson + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + to be treated with active ingredient role - + - - + + + guar gum + + Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder. + Helen Parkinson + http://en.wikipedia.org/wiki/Guar_gum + guar gum + + + + + + + + + Berichrom(r) Antithrombin III (A) Kit + + For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution + Person:Alan Ruttenberg + WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06 + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Berichrom(r) Antithrombin III (A) Kit + + + + + + + + - - - - - - - - - - - - + + - administration of material to specimen - Staining cells in a tissue slice with a dye. + micro electrode + A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus - The directed combination of a material entity with a specimen. - Bjoern Peters - Bjoern Peters - administration of material to specimen + An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system. + Helen Parkinson, Jessica Turner, Dirk Derom + micro electrode measuring device + Jessica Turner, Dirk Derom + micro electrode - + - - - device creation objective + + + fucoidan - an objective which aims to create a device with a specified function - PERSON: Helen Parkinson - OBI - device creation objective + Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). + Helen Parkinson + http://en.wikipedia.org/wiki/Fucoidan + fucoidan - + - - - growth environment - - The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. - Right now this may be incomplete. Should also cover e.g. sound, light as well. - PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters - OBI group - growth environment + + + + + + + + + + + + + + + calibration + the process of using pH buffer adjust a pH meter + + A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements. + GROUP: OBI Philly workshop + WEB:http://en.wikipedia.org/wiki/calibration + calibration - + - - - questionnaire + + + + + + + + + + + + + + + + + + + + + + + + + + + anticoagulant tube storage of blood specimen - A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. - JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. -JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. - Need to clarify if this is a document or a directive information entity (or what their connection is)) - PERSON: Jessica Turner - Merriam-Webster - questionnaire + Storage of a blood specimen in a tube with anticoagulant + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + anticoagulant tube storage of blood specimen - + - - + + @@ -21139,7 +26085,14 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + + + + + + + + @@ -21150,7 +26103,12 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + + + + + + @@ -21165,370 +26123,316 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - - + + + + + + + - Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)" + activated partial thromboplastin time assay + The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660) - An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. - Alan Ruttenberg - Gully Burns (orcid:0000-0003-1493-865X) - Jessica Turner - PMID:5146491 - url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory - Edinburgh handedness assay + An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. + There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant). + Alan Ruttenberg + OBI call + aPTT assay + url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310 + activated partial thromboplastin time assay - + - - + + - - + + - Faraday cage + filled capsule - A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. - PERSON:Bjoern Peters - Faraday shield - Wikipedia http://en.wikipedia.org/wiki/Faraday_cage - isolation function? HP - Faraday cage + A pill in the form of a small rounded gelatinous container with medicine inside. + Person:Alan Ruttenberg + http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + filled capsule - + - - + + + + + + + + + + + + + + + + + single blind study execution + + A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated + Person:Alan Ruttenberg + http://clinicaltrials.gov/ct2/info/glossary#single + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + single blind study execution + + + + + + + + - - + + - - + + + + + + + - agar stab storage + thrombin time assay + PMID:19696660#The thrombin time was determined using thromboclotin assay kit. - a storage process with input cell culture and agar and output agar stab for long time storage - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - need to specify that agar is one of input for this process - agar stab storage + An assay that measures the time between the addition of the thrombin and the clot formation in plasma. + Alan Ruttenberg + url:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 + thrombin time assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID:16453415 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse CL3 - RNA ontology - RNASE CL3 structure mapping assay + + + recombinant YAC cloning + Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21 + + Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material + Helen Parkinson + http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 + recombinant YAC cloning - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID:2422386 and PMID:2446263 - - A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure - Philippe Rocca-Serra - single nucleotide resolution mapping assay using CMCT probe - RNA ontology - CMCT structure mapping assay + + + to be treated with placebo role + + A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + to be treated with placebo role - + - + - - - - - - - - + + - image acquisition - Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel - - A planned process that captures an image of an object. - PERSON: Jie Zheng - image acquisition - image creation + treatment portion of study execution + + A planned process, part of a study design execution, during which the treatment of subjects is ongoing + 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + treatment portion of study execution - + - - - - - - - - - - - - - - - - - - - - - - - - - - PMID:6209709 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Fe-MP probe - RNA ontology - MPE-Fe(II) structure mapping assay + + + pill + + A dose of medicine or placebo in the form of a small pellet. + Person:Alan Ruttenberg + http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + pill - + - + + + research organization + The SALK institute is a research organization. + + An organization formed with a goal to have its members conduct investigations + Person:Bjoern Peters + research organization + + + + + + + + obsolete_primary structure of sequence macromolecule - A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context. - PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum - - obsolete_qualitative binding detection assay + A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds + Person:Bjoern Peters + + obsolete_primary structure of sequence macromolecule true - + - - - + + + DNA residue methylation + + a quality of a DNA residue that has a methyl group attached to it + DNA residue methylation + + + + + + + + + - - - - - - + + - - - - - - - - nucleic acid extract + + measurement device + A ruler, a microarray scanner, a Geiger counter. + + A device in which a measure function inheres. + GROUP:OBI Philly workshop + OBI + measurement device + + + + + + + + + high molecular weight DNA extract + Extraction of chromosomal DNA from mammalian cells by first isolating nucei - An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. - PERSON: Jie Zheng - UPenn Group - nucleic acid extract + The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. + PERSON:Chris Stoeckert + OBI + high molecular weight DNA extract - + - - - - - - + + + + - - + + - - - - - - - - - - - - - - - + + - + + + + + manufacturer + + A person or organization that has a manufacturer role + manufacturer + + + + + + + + + + + + - PMID:7002606 and PMID:2446263 - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using ENU probe - RNA ontology - ENU structure mapping assay + test tube + + A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material + Bjoern Peters + collection tube + sample tube + http://en.wikipedia.org/wiki/Test_tube + test tube - + - - - + + @@ -21536,44 +26440,24 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - - - - - - - - - - - - - - - + - - - - - - - + - - + + @@ -21581,206 +26465,300 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - - + + + oral ingestion of pill + + An adding a material entity to target with the entity is a pill and the target is the mouth + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + oral ingestion of pill + + + + + + + + - - + + - - PMID:7031604 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse V1 - RNA ontology - RNASE V1 structure mapping assay + + + material maintenance + + a process with that achieves the objective to maintain some or all of the characteristics of an input material over time + material maintenance - + - - + + - - - - - - - - - + + - - + + + labeled oligonucleotide + + + a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide + 2010-01-31: Philippe Rocca-Serra +placeholder + Person: Philippe Rocca-Serra + labeled oligonucleotide + + + + + + + + - - - + + - - + + - + + + + + + + + unblinding process + + The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + unblinding process + + + + + + + + + + + + - single nucleotide resolution mapping assay using Kethoxal probe - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe - Philippe Rocca-Serra - RNA ontology - kethoxal structure mapping assay + subject agrees they understand informed consent document + + A process in which a subject receives an informed consent document and agrees that they have understood it + 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + subject agrees they understand informed consent document - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - - + + - - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. - Philippe Rocca-Serra - RNAO and OBI - https://github.com/obi-ontology/obi/issues/808 - single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing + + informing subject of study arm + + A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound. + 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort + Person:Alan Ruttenberg + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + informing subject of study arm - + - - + + - - - - - - - - - + + - - + + - + Sysmex CA-6000 Coagulation Analyzer + + The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays + Person:Alan Ruttenberg + web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 + 2009/09/28 Alan Ruttenberg. Fucoidan-use-case + Sysmex CA-6000 Coagulation Analyzer + + + + + + + + + obsolete hospital + human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660] + + A medical organization at which sick or injured people are given clinical care + Person:Alan Ruttenberg + Person:Helen Parkinson + modified from the wording of the wordnet definition; http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n + + https://github.com/obi-ontology/obi/issues/1295 + + obsolete hospital + true + + + + + + + + - + - - + + - - PMID:6159633 and PMID:2446263 - - A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using DMS probe - RNA Ontology - DMS structure mapping assay + + + primary structure of RNA molecule + + The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together + Person:Bjoern Peters + primary structure of RNA molecule - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + test substance role + fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally + + A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation + Person:Alan Ruttenberg + Group:OBI + test substance role + + + + + + + + + polyA RNA extraction + + A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + polyA RNA extraction + + + + + + + + + organellar RNA extraction + + A RNA extraction process in which the desired output material is RNA in the organelle(s). + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + organellar RNA extraction + + + + + + + + + obsolete_diethyl pyrocarbonate + + + obsolete_diethyl pyrocarbonate + true + + + + + + + + + record of missing knowledge + A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. + + An information content entity created to indicate that information about something is not available to the person recording it. + This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. + Bjoern Peters + + record of missing knowledge + + + + + + + + @@ -21789,10 +26767,10 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - + @@ -21800,185 +26778,116 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - - - - - - - - - - - - PMID:3773731 - - A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure - Philippe Rocca-Serra - DNAse footprinting assay - single nucleotide resolution mapping assay using DNAse I - RNA ontology - DNASE 1 structure mapping assay + western blot assay + Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest. + + An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. + IEDB + Philippe Rocca-Serra + IEDB + Philippe Rocca-Serra + western blot assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. - Philippe Rocca-Serra - RNAO and OBI - single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing + + + total RNA extraction + + A RNA extraction process in which total cellular and organelle RNA are extracted. + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + + total RNA extraction - + - - - - - - - - - - - - - - - + + + obsolete intracellular material detection by flow cytometry assay + + An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. + + + intracellular staining + obsolete intracellular material detection by flow cytometry assay + true + + + + + + + + - - + + + complementary nucleotide probe role + A primer in a PCR reaction. A probe on an Affymetrix chip. + + A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence + PERSON:Bjoern Peters + complementary nucleotide probe role + + + + + + + + - - - - - - - + + - PMID:2843807 - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Rhodium probe - RNA ontology - Rhodium DNA structure mapping assay + record of unknown sex + A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record. + + a record indicating that the biological sex of an organism is not known. + I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement. + Bjoern Peters + record of unknown sex - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + cytoplasmic RNA extraction + + A RNA extraction process in which the desired output material is RNA in the cytoplasm. + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + cytoplasmic RNA extraction + + + + + + + + @@ -21987,10 +26896,10 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - + @@ -21998,7 +26907,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -22006,108 +26915,60 @@ JZ: based on textual definition of edited document, it can be defined as N&S - - - - - - + - PMID:7527340 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNA adenosine deaminase I - RNA ontology - RNA ADA I RNA structure mapping assay + northern blot assay + The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay. + + An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. + Philippe Rocca-Serra + Richard Scheuermann + northern blot + northern blot assay - + - - - - - - - - - - - - - - - - - - - - - + + + Likelihood-ratio test + + Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models. + Tina Boussard + Likelihood-ratio test + + + + + + + + - - - - - - - + + - PMID:2686708 - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Lead probe - RNA ontology - Lead structure mapping assay + nuclear RNA extract + Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) + + A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + nuclear RNA extract - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -22116,10 +26977,10 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - + @@ -22127,88 +26988,144 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + + 96-well neutralization assay + + A serum neutralization of viral infectivity assay which is performed in a 96-well plate. + Bjoern Peters + Melanie Courtot + microneutralization assay + 96-well neutralization assay + + + + + + + + - - - - - - + - PMID:6207483 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse T2 - RNA ontology - RNASE T2 structure mapping assay + establishing cancer cell line + Establishment of HeLa immortal cell line + + is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal + + Helen Parkinson + establishing cancer cell line - + - - - - An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. - Bjoern Peters - David Osumi Sutherland - gene dosage assay + + + pattern matching objective + + A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. + Tina Boussard + http://en.wikipedia.org/wiki/Pattern_matching + pattern matching objective - + - - + + - - + + + polyA RNA extract + Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) + + A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + polyA RNA extract + + + + + + + + + + + + + + + + + + + + + + + + single-nucleotide-resolution nucleic acid structure mapping assay + + An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. + Philippe Rocca-Serra + RNAO + single-nucleotide-resolution nucleic acid structure mapping assay + + + + + + + + - - + + - - - - - - + - PMID: 7862644 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Fe-BABE probe - RNA ontology - Fe-BABE RNA structure mapping assay + viral hemagglutination assay + Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells. + + An assay that quantifies viruses by their hemagglutination activity. + Bjoern Peters + Melanie Courtot + Randi Vita + HA + HI + viral haemagglutinin assay + url:http://en.wikipedia.org/wiki/Hemagglutination_assay + viral hemagglutination assay - + - - + + @@ -22220,7 +27137,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -22231,7 +27148,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -22254,7 +27171,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -22262,7 +27179,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -22273,401 +27190,506 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - PMID:409999 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse U2 - RNA ontology - RNASE U2 structure mapping assay + serum neutralization of viral infectivity assay + + An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. + Bjoern Peters + Melanie Courtot + influenza neutralization assay + url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/ + serum neutralization of viral infectivity assay - + - - - + + - - + + + + + + + + + + + + + + + + + + + + + + - - Determination of KD value for an antibody binding a protein using a BIACORE assay. - - A binding assay where the specified output is a binding constant - Bjoern Peters - Jason Greenbaum - Randi Vita - IEDB - binding constant determination assay + + + + pre-mortem specimen + material obtained through a liver biopsy from a human patient + + a specimen that was taken from a live organism + Bjoern Peters + MO_705 premortem + pre-mortem specimen - + - - - - - - - - - - - - - - - - - - - - - - - - - - PMID: 15796531 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe - Philippe Rocca-Serra - SHAPE mapping assay - single nucleotide resolution mapping assay using NMIA probe - RNA ontology - NMIA RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acid polymers with complementary probes + Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays. + + An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. + IEDB + IEDB + detection of specific nucleic acid polymers with complementary probes - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + - - + + + viral hemagglutination inhibition assay + Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody. + + An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors. + Bjoern Peters + Melanie Courtot + Randi Vita + HAI + HIA + biological activity + hemagglutination inhibition + viral haemagglutinin inhibition assay + OBI branch derived + viral hemagglutination inhibition assay + + + + + + + + - - - - - - - + + - PMID:10772868 - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Terbium probe - RNA ontology - Terbium RNA structure mapping assay + cytoplasmic RNA extract + Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) + + A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + cytoplasmic RNA extract - + - - + + - - + + - - - - - - - + - feature extraction + cell line immortalization + Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs - A planed process with objective of obtaining quantified values from an image. - PERSON: Jie Zheng - MO_928: feature_extraction - - feature extraction + an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line + 4-20-13 MHB: This class was repositioned as a child of 'establishing cell line', based on the existing definition ("the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro"), and examples and other annotations indicating the intent to describe a process through which a new immortal cell line is established from an existing mortal cell line using genetic modification techniques. The definition above was modified to clarify this perspective. + Bjoern Peters + 'establishing immortal cell line through directed genetic modification' + OBI + A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line. + cell line immortalization - + - - - - - - - - - - - - - - - + + + random primed DNA labeling + PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. +Methods Mol Biol. 1996;58:27-9. + + a labeling in which random primers are used to uniformly label input DNA + need to add Klenow subunit of DNA polymerase I under material entity + Person: Bjoern Peters +Person: Chris Stoeckert + Person: Philippe Rocca-Serra + PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13. + random primed DNA labeling + + + + + + + + - - + + - - - - - - - + + - PMID:2501870 - - A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe - Philippe Rocca-Serra - MOHCA assay - OH footprinting assay - single nucleotide resolution mapping assay using OH-radical probe - RNA ontology - OH-radical structure mapping assay + RNA extract + + an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + Group: UPenn Group + RNA extract - + - - - + + + - - - - - - - - - - - - + + - + - - - - - - - - - + + + + - - + + cell-cell killing assay + Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. + + A cytometry assay that monitors a cell population to track how many are killed by other cells. + IEDB + IEDB + cell-cell killing assay + + + + + + + + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - PMID:114514 - - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using RNAse T1 - RNA ontology - RNASE T1 structure mapping assay + + in vivo cell killing assay + Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells. + + A cell killing assay that measures if and how many target cells are killed within an organism. + IEDB + IEDB + in vivo cell killing assay - + - - - - - - - - - - - - - - - array image acquisition - - An image creation process that generate an image from the array. - PERSON: Jie Zheng - array image acquisition - MO_929: image_acquisition - array image creation + + + secondary structure of sequence macromolecule + + A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. +Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford. + 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO + Person: Philippe Rocca-Serra + Wikipedia + secondary structure of sequence macromolecule - + - - - - - - - - - - - - - light emission device - A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) + + + nuclear RNA extraction - A device which has a function to emit light. - Person:Helen Parkinson - OBI - light emission device + A RNA extraction process in which the desired output material is RNA in the nucleus. + Person: Chris Stoeckert + Person: Jie Zheng + UPenn Group + nuclear RNA extraction - + - - - - - - - - - - - - - perturbation device - - A homogenizer is a perturbation device. - - A perturbation device is a device which is designed to perform a perturb function - Helen Parkinson - OBI Vancouver workshop 2010 - PERSON: Helen Parkinson - perturbation device + + + + + + + + + survival curve + + A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. + PERSON:Chris Stoeckert + PERSON:James Malone + PERSON:Melanie Courtot + WEB: http://www.graphpad.com/www/book/survive.htm + survival curve - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - + + + + - environmental control device - A growth chamber is an environmental control device. + cell proliferation assay + Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. - An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. - Helen Parkinson - OBI - environmental control device + A cytometry assay which measures the degreee to which input cells are replicating. + IEDB + IEDB + cell proliferation assay - + - - + + @@ -22679,7 +27701,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -22690,7 +27712,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -22710,10 +27732,10 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - + @@ -22721,113 +27743,165 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + + + + + + + + + + + + + + + + + + + + + + + + + + - + - PMID:363143 - - A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. - Philippe Rocca-Serra - single nucleotide resolution mapping assay using Nuclease S1 - RNA ontology - Nuclease S1 structure mapping assay - - - - - - - - - specimen fixation function - e.g the function of a bar code reader used to read slide bar codes - - a function that allows specific identification of individual speciment from one another. - EAGLE-I - specimen fixation function + Southern blot assay + PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. + + An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity. + Marcus Chibucos + Philippe Rocca-Serra + Southern blot + OBI + Southern blot assay - + - - - - A specimen fixation function is a function that holds or fastens an entity in a fixed position. - EAGLE-I - - obsolete_specimen fixation function - true + + + + + + + + + real time polymerase chain reaction assay + + An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. + Bjoern Peters + Melanie Courtot + Q-PCR + kinetic polymerase chain reaction + qPCR + quantitative real time polymerase chain reaction + url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction + real time polymerase chain reaction assay - + - - + + - - - - - - - - - + + - - + + + protein extract + PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. +J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. + + a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, + Person: Philippe Rocca-Serra + OBI & wikipedia + protein extract + + + + + + + + - - - - - - - + + - PMID:3016894 - - A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe - Philippe Rocca-Serra - RNA Ontology - Ruthenium structure mapping assay + total RNA extract + Extraction of total RNA from cells with Qiagen mini RNeasy kit. + + A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + total RNA extract - + - + + + secondary structure of RNA molecule + PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. + + + 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO + Person: Philippe Rocca-Serra + secondary structure of RNA molecule + + + + + + + - + + + + + + + + @@ -22842,687 +27916,1197 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + - PMID:10573122 and PMID: 18369975 + DEPC structure mapping assay + PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. - A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity - Philippe Rocca-Serra - RNA ontology - inline probing RNA structure mapping assay - - - - - - - - - current amplification function - - A current amplification function is an amplification function that increases the amplitude of a current. - EAGLE-I - current amplification function + A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe + Philippe Rocca-Serra + RNA ontology + DEPC structure mapping assay - + - - - stabilization function - - - A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity. - EAGLE-I - isolation function - stabilization function + + + + + + + + + organellar RNA extract + Extraction of organellar RNA from plant cells using organellar RNA binding protein. + + A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + organellar RNA extract - + - - - pump function - - a transfer unction where the transfer requires work to move the entity, often against a gradient. - EAGLE-I - pump function + + + + + + + + + + + + + + + + + + + + + + + + + + + + + post mortem specimen + the spleen taken from a dead mouse + + a specimen that was taken from a dead organism + Bjoern Peters + MO_416 postmortem + post mortem specimen - + - - - cell transfer function - A cell harvester has a cell transfer function. - - is a transfer function that displaces cells from one place to another - EAGLE-I - cell transfer function + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro cell killing assay + Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. + + A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. + IEDB + IEDB + in vitro cell killing assay - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + - - + + - angiograph + reporter cell line analyte detection bioassay + CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant. - A device that records the patterns of pulse waves inside blood vessels. - PERSON: Erik Segerdell - http://medical-dictionary.thefreedictionary.com/angiograph - angiograph + An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. + IEDB + IEDB + reporter cell line analyte detection bioassay - + - - - - - - - - - capillary blotter + + + sequence feature annotation - A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed. - PERSON: Erik Segerdell - http://www.biometra.de/ - capillary blotter + Information about a sequence region + Bjoern Peters + Bjoern Peters + place holder for sequence ontology term + sequence feature annotation - + - - - - - - - - + + - - + + - bioreactor + induced hemagglutination - A device or system that supports a biologically active environment. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Bioreactor - bioreactor + The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances + MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO. +Dev call Nov 22, 2010: To reflect this, the term's label has been updated to 'induced hemagglutination'. + person: Bjoern Peters + person: Melanie Courtot + hemeagglutination + WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination + induced hemagglutination - + - - + + - - + + - pH meter + supplying + Jackson Labs supplies mouse strains. - A device that is used to measure the pH (acidity or alkalinity) of a liquid. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/PH_meter - pH meter + The planned process of providing material entities +to be used in an investigation. + Jennifer Fostel + Jennifer Fostel + 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. + supplying - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - digital camera + labeled DNA extract - An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Digital_camera - digital camera + a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. + Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. +Added duirng Mar 1, 2010 dev call + Group: OBI group + Group: OBI group + labeled DNA extract - + - - + + - - + + - chip spotting device + cloacal specimen + type of sample used in the PCIRN influenza network - A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray. - PERSON: Erik Segerdell - United States Patent 7416705 - chip spotting device + A specimen obtained by inserting a swab deeply into the vent of the cloaca of +an organism and vigorously swabbing the wall. The swab should be deeply +stained with fecal material and is then placed in transport medium. + PERSON: Melanie Courtot + WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf + cloacal specimen - + - - - RNA extraction/purification instrument + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + radio immuno assay + To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. - A device that is used to isolate and collect RNA for subsequent molecular analysis. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - RNA extraction/purification instrument + An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. + IEDB + IEDB + radio immuno assay - + - - + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + - DNA extract + real time reverse-transcription polymerase chain reaction assay - The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. - Person: Jie Zheng - Group: UPenn group - DNA extract + An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. + Bjoern Peters + Melanie Courtot + RRT-PCR + RT-rt PCR + qRT-PCR + real time reverse-transcription polymerase chain reaction assay - + - - - two-photon laser/detector + + + + + + + + + + + + + + + + + + + + + + + + + + + X-ray crystallography 3D molecular structure determination assay + Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. - A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy - two-photon laser/detector + A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. + IEDB + IEDB + X-ray crystallography 3D molecular structure determination assay - + - - + + - - + + - electrophoresis system - - A device that moves charged particles through a medium by using an electric field induced by electrodes. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Category:Electrophoresis - electrophoresis system - - - - - - - - - - + + + + + + + - PET synthesizer + promoter activity detection by reporter gene assay + A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color. - A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - PET synthesizer + An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. + IEDB + IEDB + promoter activity detection by reporter gene assay - + - - + + - - + + - spinning-disk confocal microscope - - A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Nipkow_disk - spinning-disk confocal microscope - - - - - - - - - DNA synthesizer + nasopharyngeal aspirate specimen + type of sample used in the PCIRN influenza network - An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. - PERSON: Erik Segerdell - http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers - DNA synthesizer + A speciemn which derives from nasopharyngeal mucosa after +aspiration. + PERSON: Melanie Courtot + WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf + nasopharyngeal aspirate specimen - - - - - high performance liquid chromatography instrument - - A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/High_performance_liquid_chromatography - high performance liquid chromatography instrument - - + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - microplate reader + freezing storage + a fozen pellet used for later assay - A measurement device that detects biological, chemical or physical events of samples in microtiter plates. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Plate_reader - microplate reader + A storage process in temperature that maintenance the frozen status of the stored entities. + 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" +2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. +Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen. + Person: Alan Ruttenberg, Mathias Brochhausen + MO_481 frozen_storage + OBI + freezing storage - + - - - ELISA microplate reader + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + flow cytometry assay + Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody. - A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). - PERSON: Erik Segerdell - PERSON: Erik Segerdell - ELISA microplate reader + A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. + IEDB + FACS + IEDB + flow cytometry assay - + - - + + - - + + + + + + + + - spot cutter + nasal swab specimen + type of sample used in the PCIRN influenza network - A robotic device that is used to excise spots from gels. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - spot cutter + A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of +exudate and epithelial debris for microbiological or cellular examination. + PERSON: Melanie Courtot + WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf + nasal swab specimen - + - - + + - - - - + + + + + + + + + + + + + Dulbecco's modified Eagle medium + + A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. + Logical definition should contain all components listed in textual definition at some point. + PERSON:Bjoern Peters + D-MEM + DMEM + Dulbecco's modified Eagle medium + + + + + + + + - - + + - microwave synthesis system + animal euthanization + Rats were euthanized with CO2 - A device that is used to apply microwave irradiation to chemical reactions. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Microwave_chemistry - microwave synthesis system + A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject + Helen Parkinson and Melissa Haendel + animal sacrifice + Melissa Haendel + may later be refined with more specific list of organisms + animal euthanization - + - - - - - - - - - densitometer + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay + Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture. - A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Densitometer - densitometer + An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest. + IEDB + Luminex assay + IEDB + cytometric bead array assay - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + - - + + - automatic staining machine + labeled RNA extract - A device that is used to automatically stain tissue sections on slides or tissue specimens. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - automatic staining machine + a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. + Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. +Added duirng Mar 1, 2010 dev call + Group: OBI group + Group: OBI group + labeled RNA extract - + - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + frozen specimen + Frozen blood plasma + + A specimen that has been frozen in order to store it. + Person:Alan Ruttenberg + MO_610 frozen_sample + frozen specimen + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + - automatic tissue processor + surface plasmon resonance binding assay + Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow. - A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. - PERSON: Erik Segerdell - United States Patent 3762362 - automatic tissue processor + A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. + IEDB + IEDB + surface plasmon resonance binding assay - + - - - + + + + + + + + + + + + + + + + + labeled specimen + + A specimen that has been modified in order to be able to detect it in future experiments + added during call 3/1/2010 + OBI group + labeled specimen + + + + + + + + - - + + - - stereo microscope - - An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope - stereo microscope + + + infectious agent + + is a material entity bearing the disposition to infect an organism + IEDB + IEDB + infectious agent - + - - - top loading balance - - A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - top loading balance + + + obsolete_ambidexterious handedness + + + obsolete_ambidexterious handedness + true - + - - + + - - + + - perfusion station + + + + + + + lyophilization storage + + + a storage process with input material entity and output freeze dried material for long time storage + PERSON: Chris Stoeckert + PERSON: Jie Zheng + + can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed + lyophilization storage + + + + + + + + + material combination function + A stirrer has a material combination function - A device or system in which perfusion units are integrated. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - perfusion station + A material separation function is a function that decreases the resolution between two or more material entities. + Helen Parkinson + OBI + material combination function - + - + + + obsolete_training service provider role + EBI provides training on databases and tools and has a training service provider role + + a service provider role which is realized by a servicer provider organization performing some training + PERSON:Helen Parkinson + OBI + + obsolete_training service provider role + true + + + + + + + - - - - - - - SPECT scanner + calorimeter - A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography - SPECT scanner + A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. + PERSON:Bjoern Peters + calorimetry instrument? + http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm + calorimeter - + - - + + + + + + + + + + + + + + + + - - + + - + - - + + + + + + + - + - array manufacturer role + study intervention - a manufacturer role which is played by the person or organization that manufactured the array - PERSON: Chris Stoeckert, Jie Zheng - MO_695 array_manufacturer - array manufacturer role + the part of the execution of an intervention design study which is varied between two or more subjects in the study + PERSON: Bjoern Peters + GROUP: OBI + study intervention - + - - - - - - - - - scintillation counter - - A device that is used to measure ionizing radiation. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Scintillation_counter - scintillation counter + + + + + + + + + + + + + material separation device + flow cytometer + + A device with a separation function realized in a planed process + material separation device - + - - + + - + - programmable array microscope + positron emission tomography scanner - A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. - PERSON: Erik Segerdell - Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8 - programmable array microscope + A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. + PERSON:Bjoern Peters + PET scanner? + http://en.wikipedia.org/wiki/Positron_emission_tomography + positron emission tomography scanner - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - cryostat - - A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Cryostat - cryostat + intramuscular injection + + is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe + intramuscular injection - + - + @@ -23530,361 +29114,330 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microtome knife maker + micromanipulator - A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - microtome knife maker + A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. + PERSON:Bjoern Peters + http://en.wikipedia.org/wiki/Micromanipulator + micromanipulator - + - - - - - - - - - cryofixation device - - A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Cryofixation - cryofixation device + + + obsolete_material access provider role + A person or organization who provides access to a DNA sequencer. + + a service provider role which is realized by a servicer provider organization performing access to some material + PERSON:Helen Parkinson + OBI + + obsolete_material access provider role + true - + - - - - - - - - - - - - - - - hybridization oven - - A device that creates an appropriate environment for nucleic acid hybridization. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - hybridization oven + + + obsolete_left handedness + + + obsolete_left handedness + true - + - - - - - - - - - - - - - - + + - - + + - incubator shaker + categorical measurement datum - An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). - PERSON: Erik Segerdell - PERSON: Erik Segerdell - incubator shaker + A measurement datum that is reported on a categorical scale + Bjoern Peters + nominal mesurement datum + Bjoern Peters + + categorical measurement datum - + - - - - - - - - - + + - - + + - - small-animal image acquisition device - - A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - small-animal image acquisition device + + + training process + e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility + + a process that achieves a training objective + training process - + - - - - - - - - - - - - - - - infrared image acquisition device + + + optical microscope - An image acquisition device that is responsive to an infrared emissive target within a given field of view. - PERSON: Erik Segerdell - United States Patent 4107530 - infrared image acquisition device + A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range + PERSON:Bjoern Peters + optical microscope - + - - + + - - + + + + + + + + + - confocal microscope + service consumer role + A biologist who uses a sequencing services fulfills the role of a service consumer - A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Confocal_microscopy - confocal microscope + a role which inheres in a person who uses a service + Person:Helen Parkinson + OBI + service consumer role - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - patch clamp device - - A device used in electrophysiology that allows the study of single or multiple ion channels in cells. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Patch_clamp - patch clamp device + intradermal injection + + is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + intradermal injection - + - - + + - - + + - - + + + + + + + + + + + + - gel imaging system - - A device that is used to acquire images of laboratory gels. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - gel imaging system - - - - - - - - - - + + - protein separation apparatus - - A device that is used for the separation of proteins. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - protein separation apparatus - - - - - - - - - multichannel electronic pipette + chemical cleavage + PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. +Biochimie. 2010 Feb 18. - A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations. - PERSON: Erik Segerdell - http://www.faqs.org/patents/app/20090196797 - multichannel electronic pipette + chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent + PERSON:Philippe Rocca-Serra + RNA ontology group + chemical cleavage - + - - + + - - + + + + + + + + + + + + + - vitrification apparatus + handedness assay + The Edinburgh handedness assay is a specific method of determing handedness - A device that is used to effect the transition of a substance into a glass. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Glass_transition - vitrification apparatus + An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. + Helen Parkinson + handedness test + url:http://en.wikipedia.org/wiki/Handedness + handedness assay - + - + - - - - - - - + - radiography instrument + vibration isolation table - An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Medical_radiography - radiography instrument + A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor. + PERSON:Bjoern Peters + United States Patent 6877711 + vibration isolation table - + - - - - - - - - - - - - - - - radiation measurement device - - A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - radiation measurement device + + + sterilization function + + a function to remove viable organisms from an input material + sterilization function - + - - + + - - + + + + + + + + + - - + + - lyophilizer - - A device that is used to freeze dry material. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Freeze_drying - lyophilizer - - - - - - - - - tandem mass spectrometer - - A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. - PERSON: Erik Segerdell - http://goldbook.iupac.org/T06250.html - tandem mass spectrometer + service provider role + Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. + + is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person + PERSON:Helen Parkinson + service provider role - + - + @@ -23892,1638 +29445,1677 @@ JZ: based on textual definition of edited document, it can be defined as N&S - microhardness tester - - A hardness testing device that is used in light-optical microscopes. - PERSON: Erik Segerdell - United States Patent 4611487 - microhardness tester - - - - - - - - - multimode microplate reader + oscilloscope - A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - multimode microplate reader + A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis). + PERSON:Bjoern Peters + http://en.wikipedia.org/wiki/Oscilloscope + oscilloscope - + - - - mechanical balance - - A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). - PERSON: Erik Segerdell - http://www.britannica.com/EBchecked/topic/49765/balance - mechanical balance + + + accessed material role + the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism + + is realized in a planned process where the bearer participates + AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it + accessed material role - + - - - computer cluster - - A group of linked computers, working together closely so that in many respects they form a single computer. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Cluster_(computing) - computer cluster + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + paraffin specimen + liver tissue embedded in paraffin + + a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_990 paraffin_sample + paraffin specimen - + - - + + - - + + + + + + + + + + + + + + + + + + + - microtome knife sharpener + compound treatment design - A device that is used to sharpen knives used in microtomy. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - microtome knife sharpener + an intervention design in which the treatment is the administration of a compound + This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. + PERSON: Bjoern Peters + MO_555 compound_treatment_design + compound treatment design - + - - + + + + + + + + + + + + + + + + + + + + + + + - - + + - plate shaker - - A device that provides shaking motion for microplates. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - plate shaker + oral administration + + An administering substance in vivo into the mouth of an organism + PERSON: Melanie Courtot + oral administration - + - - - - - - - - - coagulation analyzer - - A device for automatically analyzing blood coagulation in a clinical laboratory. - PERSON: Erik Segerdell - United States Patent 5439646 - coagulation analyzer + + + + + + + + + + processed specimen + A tissue sample that has been sliced and stained for a histology study. +A blood specimen that has been centrifuged to obtain the white blood cells. + + A specimen that has been intentionally physically modified. + Bjoern Peters + Bjoern Peters + A tissue sample that has been sliced and stained for a histology study. + processed specimen - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - laser capture microdissection microscope - - A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. - PERSON: Erik Segerdell - http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine - laser capture microdissection microscope + subcutaneous injection + + is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + subcutaneous injection - + - - + + - liquid extraction robot + electrode puller - A liquid handling device that provides automatic liquid extraction. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - liquid extraction robot + A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube. + PERSON:Bjoern Peters + http://faculty.plattsburgh.edu/donald.slish/Puller1.html + electrode puller - + - - + + + obsolete_handedness + + + + obsolete_handedness + true + + + + + + + + - - + + - - + + + + + + + - ultrasound machine - - A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Sonography - ultrasound machine + self reported handedness assessment + + An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. + self reported handedness assessment - + - + - + - + + + + + + - immunoblot scanner - - A device that is used for the imaging of immunoblots. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - immunoblot scanner - - - - - - - - - microcentrifuge - - A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Laboratory_centrifuge - microcentrifuge + vibrotome + + A preparation device that uses a vibrating razor blade to cut through tissue. + vibrotome - + - - - electronic repeater pipette + + + reagent application function + An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. - A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. - PERSON: Erik Segerdell - http://www.faqs.org/patents/app/20090196797 - electronic repeater pipette + A function that is realized when a reagent is automatically added to some research material. + PERSON: Nicole Vasilevsky, Matthew Brush + PERSON: Nicole Vasilevsky, Matthew Brush + 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people? + reagent application function - + - - - electron paramagnetic resonance spectrometer + + + addition of molecular tracer function + Immunohistochemical labeling of tissue sections by an autostainer staining system. - An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance - electron paramagnetic resonance spectrometer + A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. + PERSON: Nicole Vasilevsky, Matthew Brush + PERSON: Nicole Vasilevsky, Matthew Brush + addition of molecular tracer function - + - - - - - - - - - rocker + + + training objective + A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package - A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). - PERSON: Erik Segerdell - PERSON: Erik Segerdell - rocker + An objective specification which is fulfilled by the provision of some training. + Helen Parkinson + OBI + training objective - + - - - analytical balance + + + categorical label + The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. - A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Weighing_scale - analytical balance + A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. + Bjoern Peters + Bjoern Peters + categorical label - + - - - - - - - - - scanning force microscope - - A microscope that forms images of surfaces using a physical probe that scans the specimen. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Scanning_probe_microscopy - scanning force microscope + + + in live cell assay + + An assay in which a measurement is made by observing entities located in a live cell. + in live cell assay - + - - - pulsed-field gel electrophoresis system - - A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis - pulsed-field gel electrophoresis system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lyophilized specimen + freezing dried DNA + + a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_589 freeze_dried_sample + lyophilized specimen - + - - + + - - + + + + + + + + + + + + + + + + + + + + + + - tissue embedding station + in live organism assay + Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. - A device that is used to perform paraffin embedding of tissue specimens. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - tissue embedding station + An assay in which a measurement is made by observing entities located in an organism. + Bjoern Peters + in vivo assay + in live organism assay - + - - - - - - - - - nucleic acid sequencer - - An device that is used to determine the order of nucleotides in nucleic acid sequences. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - nucleic acid sequencer + + + + + + + + + + + + + container + + A device that can be used to restrict the location of material entities over time + 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) + PERSON: Bjoern Peters + container - + - - + + - - + + - + - bead array reader - - A device that is used to acquire and image bead array data. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - bead array reader - - + + + + + + + + + + + + device + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + +2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: +(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - +(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - - - real-time PCR machine - - An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction - real-time PCR machine +(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. + +In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + device - + - - - - - - - - - - - - - - - - - - - - - paraffin oven - - A device that is used for the warming of paraffin embedding medium. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - paraffin oven + + + dose specification + a protocol specifying to administer 1 ml of vaccine to a mouse + + a directive information entity that describes the dose that will be administered to a target + dose specification - + - - - - - - - - + + - - + + - - + + 1 - autoclave + scalar score from composite inputs - A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents. - PERSON: Erik Segerdell - J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave - autoclave + A measurement datum which is the result of combining multiple datum. For example, a mean or summary score. + JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question. + Person: Jessica Turner + questionaire score + Person: Jessica Turner + JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation? + scalar score from composite inputs - + - - - - - - - - - microplate washer - - A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? - PERSON: Erik Segerdell - http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037 - microplate washer + + + + fresh specimen + a liver freshly removed from a rat + + a specimen that is output of a specimen creation process used for an investigation without storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_730 fresh_sample + fresh specimen - + - - - - - - - - - nucleic acid extraction/purification instrument - - A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - nucleic acid extraction/purification instrument + + + obsolete_electrically powered device + + a processed material created to have a function and which requires electrical power to execute + + obsolete_electrically powered device + true - + - - - ELISA microplate washer + + + + + + + + + + + + + sequence data + example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). - PERSON: Erik Segerdell - PERSON: Erik Segerdell - ELISA microplate washer + A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + + Person:Chris Stoeckert + GROUP: OBI + sequence data - + - - - - - - - - - vacuum manifold - - A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - vacuum manifold + + + obsolete_right handedness + + + obsolete_right handedness + true - + - - - DNA extraction/purification instrument + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell-cell binding detection by flow cytometry assay + Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. - A device that is used to isolate and collect DNA for subsequent molecular analysis. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/DNA_extraction - DNA extraction/purification instrument + A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. + IEDB + IEDB + cell-cell binding detection by flow cytometry assay - + - - + + - - + + - - + + + + + + + + + + - multichannel pipette - - A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - multichannel pipette + handedness categorical measurement datum + + A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally + PERSON:Alan Ruttenberg + PERSON:Jessica Turner + handedness categorical measurement datum - + - - + + - - + + + + + + + + + + + + + + + - cell harvester + paraffin storage + - A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? - PERSON: Erik Segerdell - PERSON: Erik Segerdell - cell harvester + a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + need to specify paraffin or wax is one of specified input of the process + paraffin storage - + - - - portable fluorometer - - A compact fluorometer that can be carried or moved with ease. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - portable fluorometer + + + in container assay + + An assay in which a measurement is made by observing entities located in a container. + in container assay - + - - - gel electrophoresis system + + + obsolete_protocol service provider role + DNA sequencing of a sample by a core lab which returns data to the consumer - An electrophoresis system in which an electric field is applied to a gel matrix - PERSON: Erik Segerdell - https://en.wikipedia.org/wiki/Gel_electrophoresis - gel electrophoresis system + a service provider role which is realized by a servicer provider organization performing a protocol execution + PERSON:Helen Parkinson + + obsolete_protocol service provider role + true - + - - - + + - - - - - diffractometer - - A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Diffractometer - diffractometer - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - microdissection instrument - - A device that is used for the dissection of tissues under magnification. - PERSON: Erik Segerdell - http://medical-dictionary.thefreedictionary.com/microdissection - microdissection instrument + + + agar stab specimen + + a specimen that is output of a process that cell culture inoculated into agar for long term storage. + PERSON: Chris Stoeckert + PERSON: Jie Zheng + MO_971 agar_stab + agar stab specimen - + - + - + - micropipette puller + computed tomography scanner - A device that is used to fabricate glass micropipettes. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Micropipette - micropipette puller + An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation. + PERSON:Bjoern Peters + CT scanner + X-ray computed tomography scanner + http://en.wikipedia.org/wiki/X-ray_computed_tomography + computed tomography scanner - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - laser scanning confocal microscope - - A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy - laser scanning confocal microscope + intranasal mucosal administration + + The administration of a substance into the intranasal mucosis of an organism + PERSON: Melanie Courtot + intranasal mucosal administration - + - - - - - - - - - digital microscope - - A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Digital_microscope - digital microscope + + + dose + An organism has been injected 1ml of vaccine + + A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. + dose - + - - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - freeze substitution system + growth condition intervention design - A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins. - PERSON: Erik Segerdell - doi:10.1017/S143192760707866X - freeze substitution system + A study design in which the independent variable is the environmental condition in which the specimen is growing + PERSON: Bjoern Peters + MO_588 growth_condition_design + growth condition intervention design - + - - - - - - - - - - - - - - - micropipette - - A microinjection device that is used to measure very small volumes of liquids. - PERSON: Erik Segerdell - http://www.answers.com/topic/micropipette - micropipette + + + obsolete_DNA sequencing training service + + A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments + + obsolete_DNA sequencing training service + true - + - - - - - - - - - voltage clamp device - - A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Voltage_clamp - voltage clamp device + + + obsolete_general scalar measurement datum + + + obsolete_general scalar measurement datum + true - + - - - - - - - - - - - - - - - - - - - - - vacuum oven - - A device that heats materials in a vacuum. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - vacuum oven + + + obsolete performing a diagnosis + Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache. + + The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis + + https://github.com/obi-ontology/obi/issues/623 + obsolete performing a diagnosis + true - + - - + + - + + + + + + - slide warmer - - A device that is used to heat microscope slides. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - slide warmer + PCR instrument + + A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. + 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. + PCR instrument - + - - - capillary electrophoresis instrument - - An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Capillary_electrophoresis - capillary electrophoresis instrument + + + electron microscope + + A microscope that produces an image of an object by targeting it with an electron beam + electron microscope - + - - + + - - + + - denaturing high-performance liquid chromatography instrument - - A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis. - PERSON: Erik Segerdell - doi:10.1385/1-59259-850-1:173 - denaturing high-performance liquid chromatography instrument - - - - - - - - - agarose gel electrophoresis system - - A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis - agarose gel electrophoresis system + + + + 1 + + + Edinburgh score + + A score that measures the dominance of a person's right or left hand in everyday activities. + Person: Alan Ruttenberg + Person:Jessica Turner + PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 + WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html + Edinburgh score - + - - + + + + + + + + + + + + - - + + - - + + - balance - - A measuring instrument that is used to determine the weight or mass of an object. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Weighing_scale - balance + DNA sequencing service + + A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. + Eagle-i will supply better English definition + DNA sequencing service - + - - - - - - - - - surface plasmon resonance instrument + + + service provision objective + A sequencing centre has a service provision objective - A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles. - PERSON: Erik Segerdell - http://en.wikipedia.org/wiki/Surface_plasmon_resonance - surface plasmon resonance instrument + An objective which is fulfilled by the provision of some service e.g. a training service + Helen Parkinson + OBI + service provision objective - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - protein sequencer - - An device that is used to determine the order of amino acids in protein sequences. - PERSON: Erik Segerdell - PERSON: Erik Segerdell - protein sequencer + intravenous injection + + is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe + PERSON: Melanie Courtot + intravenous injection - + - - + + - - + + + + + + + + + + + + - X-ray source - - A device that is used to generate X-rays. - PERSON: Erik Segerdell - x-ray generator - http://en.wikipedia.org/wiki/X-ray_generator - X-ray source - - - - - - - - - liquid chromatography instrument + administration of material to specimen + Staining cells in a tissue slice with a dye. - A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated - PERSON: Matthew Brush - PERSON: Matthew Brush - liquid chromatography instrument + The directed combination of a material entity with a specimen. + Bjoern Peters + Bjoern Peters + administration of material to specimen - + - - - spike-in quality control role + + + device creation objective - a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes - PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter - MO_937 spike_quality_control - spike-in quality control role + an objective which aims to create a device with a specified function + PERSON: Helen Parkinson + OBI + device creation objective - + - - - - - - - - - individual organism identifier + + + growth environment - a CRID symbol used to distinguish one individual organism from another. - PERSON: Chris Stoeckert, Jie Zheng - MO_169 Individual - individual organism identifier + The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. + Right now this may be incomplete. Should also cover e.g. sound, light as well. + PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters + OBI group + growth environment - + - - - - - - - - - dye swap quality control role + + + questionnaire - a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes - PERSON: Chris Stoeckert, Jie Zheng - MO_524 dye_swap_quality_control - dye swap quality control role + A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. + JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. +JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. + Need to clarify if this is a document or a directive information entity (or what their connection is)) + PERSON: Jessica Turner + Merriam-Webster + questionnaire - + - - + + - + - + - - + + - - + + + + + + + + + + + + - - + + - labeled nucleic acid extract + + + + + + + Edinburgh handedness assay + Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)" - a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. - Person: Jie Zheng - labeled extract - MO_221 labeledExtract - labeled extract - labeled nucleic acid extract - - - - - - - - - binding constant - The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes". - - A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed. - 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. - PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum - binding constant + An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. + Alan Ruttenberg + Gully Burns (orcid:0000-0003-1493-865X) + Jessica Turner + PMID:5146491 + url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory + Edinburgh handedness assay - + - - - - - - - - - - - - - - - - - - - - - - Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. - A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration. - IEDB - IEDB - 3D structure determination of bound molecular complex assay + + + + + + + + + Faraday cage + + A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. + PERSON:Bjoern Peters + Faraday shield + Wikipedia http://en.wikipedia.org/wiki/Faraday_cage + isolation function? HP + Faraday cage - + - - + + - - + + - - - - - - - + + - Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. - An assay with the objective to characterize the disposition of two or more material entities to form a complex. - Bjoern Peters - Jason Greenbaum - Randi Vita - binding assay + agar stab storage + + a storage process with input cell culture and agar and output agar stab for long time storage + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + need to specify that agar is one of input for this process + agar stab storage - + - - + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + - - + + + + + + + - cell culture expansion - - a process that results in the increase of cell numbers - including grow of yeast and bacteria - PERSON: Chris Stoeckert, Jie Zheng - MO_758 grow - BP: -add it as subclass of 'cell culturing' -JZ: -No 'cell culturing' in OBI -Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process. - cell culture expansion - - - - - - - - - gene knock out - - a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. - PERSON: Chris Stoeckert, Jie Zheng - MO_771 gene_knock_out - gene knock out - - - - - - - - - gene knock in - - a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. - PERSON: Chris Stoeckert, Jie Zheng - MO_437 gene_knock_in - WEB: http://en.wikipedia.org/wiki/Gene_Knock-in - gene knock in - - - - - - - - - chromosomal substitution - - A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'. - PERSON: Chris Stoeckert, Jie Zheng - MO_995 chromosomal_substitution - chromosomal substitution + RNASE CL3 structure mapping assay + PMID:16453415 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse CL3 + RNA ontology + RNASE CL3 structure mapping assay - + - - - - - + + + + + + - - - - - - - + + + + - - - - - genetically modified material - - a material entity, organism or cell, that is the output of a genetic transformation process. - PERSON: Jie Zheng - GROUP: OBI - term is proposed by BP on Oct 25, 2010 dev call - genetically modified material - - - - - - - - + + + - - + + - + - - - - - - - - - - - - - - + + + + - transfection - - a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell - PERSON: Chris Stoeckert, Jie Zheng - MO_366 transfection - transfection - - - - - - - - - genetic transformation objective - - a material transformation objective aims to create genetically modified organism or cell - Person: Jie Zheng - Person: Jie Zheng - suggested to be added by BP and AR during Oct 25, 2010 dev call - genetic transformation objective - - - - - - - - - induced mutagenesis - - A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation. - Label and definition were clarified as per https://github.com/obi-ontology/obi/issues/1366 - PERSON: Chris Stoeckert, Jie Zheng - MO_564 induced_mutation - induced mutagenesis + CMCT structure mapping assay + PMID:2422386 and PMID:2446263 + + A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure + Philippe Rocca-Serra + single nucleotide resolution mapping assay using CMCT probe + RNA ontology + CMCT structure mapping assay - + - - - 3D structural organization datum - The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. + + + + + + + + + + + + + + + image acquisition + Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel - A measurement datum that describes the structural orientation of a material entity in 3D space. - PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters - 3D structural organization datum + A planned process that captures an image of an object. + PERSON: Jie Zheng + image acquisition + image creation - + - - - age since planting measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. - PERSON:Chris Stoeckert, Jie Zheng - MO_495 planting - Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. -Term proposed by Bjoern on Nov 8, 2010 dev call -Supported by Alan on Nov 15, 2010 dev call - age since planting measurement datum + + + + + + + + + + + + + + + + + + + + + + + + + + MPE-Fe(II) structure mapping assay + PMID:6209709 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Fe-MP probe + RNA ontology + MPE-Fe(II) structure mapping assay - + - - - age since hatching measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. - PERSON:Chris Stoeckert, Jie Zheng - MO_745 hatching - age since hatching measurement datum + + + obsolete_qualitative binding detection assay + + A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context. + PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum + + obsolete_qualitative binding detection assay + true - + - - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - - + + + nucleic acid extract - An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). - This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. - Alan Ruttenberg - age measurement assay - OBI group - age determination assay - - - - - - - - - age since egg laying measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. - PERSON:Chris Stoeckert, Jie Zheng - MO_767 egg laying - age since egg laying measurement datum - - - - - - - - - assay validation objective - - an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results - PERSON: Chris Stoeckert, Jie Zheng - GROUP: Penn Group - assay validation objective - - - - - - - - - age since germination measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. - Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. - PERSON:Chris Stoeckert, Jie Zheng - MO_590 germination - age since germination measurement datum - - - - - - - - - validation by reverse transcription PCR design - - a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results - PERSON: Chris Stoeckert, Jie Zheng - MO_986 reverse_transcription_PCR_quality_control - validation by reverse transcription PCR design + An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. + PERSON: Jie Zheng + UPenn Group + nucleic acid extract - - - - - age since eclosion measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. - PERSON:Chris Stoeckert, Jie Zheng - MO_876 eclosion - age since eclosion measurement datum - - - - - - - - - age since sowing measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. - PERSON:Chris Stoeckert, Jie Zheng - MO_748 sowing - age since sowing measurement datum - - - - - - - - - age since coitus measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. - PERSON:Chris Stoeckert, Jie Zheng - MO_783 coitus - age since coitus measurement datum - - - - - - - - - validation by real time PCR design - - a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results - PERSON: Chris Stoeckert, Jie Zheng - MO_434 real_time_PCR_quality_control - validation by real time PCR design - - - - - + - - + + - - + + + + + + + + + - age measurement datum - - A time measurement datum that is the result of measurement of age of an organism - note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. -life of bearer doesn't imply organism -this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature -age as a quality is dubious; we plan to revisit -stages in development are currently handled with controlled vocabulary, such as 2-somite stage - PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng - MO_178 Age - In MageTab file, we use -initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) -Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class - discussed on Nov 15, dev call -All subtype will be defined by textual definition now. - age measurement datum - - - - - - - - - age since fertilization measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. - Definition of fertilization comes from GO. - PERSON:Chris Stoeckert, Jie Zheng - MO_701 fertilization - age since fertilization measurement datum - - - - - - - - - age since birth measurement datum - - An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. - PERSON:Chris Stoeckert, Jie Zheng - MO_710 birth - age since birth measurement datum + + + + + + + + + + + + + + + + + + ENU structure mapping assay + PMID:7002606 and PMID:2446263 + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using ENU probe + RNA ontology + ENU structure mapping assay - + - - + + @@ -25559,188 +31151,283 @@ All subtype will be defined by textual definition now. - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - - - - - - + - - An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. - Chris Stoeckert - Jie Zheng - Penn Group - reverse transcription polymerase chain reaction assay + RNASE V1 structure mapping assay + PMID:7031604 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse V1 + RNA ontology + RNASE V1 structure mapping assay - + - - + + - - + + + + + + + + + - half life datum (t 1/2) - - The time it takes for 50% of a class of stochastic processes to occur. - Bjoern Peters - t 1/2 - Bjoern Peters - half life datum (t 1/2) - - - - - - - - - dose response curve - - A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. - Bjoern Peters; Randi Vita - dose response curve + + + + + + + + + + + + + + + + + + kethoxal structure mapping assay + single nucleotide resolution mapping assay using Kethoxal probe + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe + Philippe Rocca-Serra + RNA ontology + kethoxal structure mapping assay - + - + - + - + + + + + + + + + + + - - + + + + + + + + + + + - - - - - - - service - providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony - - A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. - Carlo; Matt - OBI workshop San Diego 2011 - service + single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. + Philippe Rocca-Serra + RNAO and OBI + https://github.com/obi-ontology/obi/issues/808 + single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing - + - - + + - + - - - - - - - + + + + - passive immunization - Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. -Transferring epitope specific T cells from one mouse into another. + + + + + + + + + + + + + + + + + + DMS structure mapping assay + PMID:6159633 and PMID:2446263 - The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. - PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum - adoptive transfer - passive immunization - - - - - - - - - selective organism creation objective - - an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. - PERSON: Chris Stoeckert, Jie Zheng - WEB: wikipedia -http://en.wikipedia.org/wiki/Cultivar -http://en.wikipedia.org/wiki/Ecotype -http://en.wikipedia.org/wiki/Strain_%28biology%29 - selective organism creation objective + A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using DMS probe + RNA Ontology + DMS structure mapping assay - + - - - Individual epitope immunization in vivo - Injection of a peptide T cell epitope into a mouse - - An immunization in which an individual epitope is administered into a host organism. - 3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here. - PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita - Individual epitope immunization in vivo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DNASE 1 structure mapping assay + PMID:3773731 + + A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure + Philippe Rocca-Serra + DNAse footprinting assay + single nucleotide resolution mapping assay using DNAse I + RNA ontology + DNASE 1 structure mapping assay - + - + - + @@ -25748,32 +31435,19 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + @@ -25784,1168 +31458,856 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - + + + + - - - - - - - - - - - - - + - - An assay that determines the sequence of an RNA molecule. - Bjoern Peters - Bjoern Peters - RNA sequencing assay + single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. + Philippe Rocca-Serra + RNAO and OBI + single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing - + - - - - - - - - + + - + - - - - - - - + + + + - - An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism. - Bjoern Peters - efficacy of in vivo intervention - efficacy of epitope intervention experiment - - - - - - - - - - An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. - Bjoern Peters - protection from infectious challenge - epitope protection from infectious challenge experiment - - - - - - - - - - + + - - + + + + + + + - half maximal effective concentration (EC50) - Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. - - half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. - - Bjoern Peters; Randi Vita - wikipedia - half maximal effective concentration (EC50) + Rhodium DNA structure mapping assay + PMID:2843807 + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Rhodium probe + RNA ontology + Rhodium DNA structure mapping assay - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - binding datum - - A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. - Bjoern Peters; Randi Vita - binding datum - - - - - - - - - negative binding datum - - A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. - negative binding datum - - - - - - - - - - An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. - Bjoern Peters - tumor burden after challenge - epitope protection from tumor challenge experiment - - - - - - - - - - An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. - Bjoern Peters - protection from challenge - epitope protection experiment - - - - - - - - + + - - + - + - - + + + + + + - - selectively maintained organism - - An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms - Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert - cultivar - ecotype - strain - MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar - selectively maintained organism - - - - - - - - - - An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. - Bjoern Peters - pathogen urden after infectious challenge - epitope protection from infectious challenge experiment based on pathogen burden - - - - - - - - + - + - Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus. - - An assay that measures the presence or amount of an infectious agent in an evaluant - Bjoern Peters - Jason Greenbaum - Randi Vita - Richard Scheuermann - infectious agent detection assay - - - - - - - - - - An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. - Bjoern Peters - exacerbation assay - epitope disease exacerbation experiment - - - - - - - - - - An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. - Bjoern Peters - host survival after challenge - epitope protection experiment based on survival + RNA ADA I RNA structure mapping assay + PMID:7527340 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNA adenosine deaminase I + RNA ontology + RNA ADA I RNA structure mapping assay - + - - - - An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. - Bjoern Peters - decreased disease symptoms after treatment - epitope treatment experiment - - - - - - - - + + - - + + + + + + + + + - - + + - half maximal inhibitory concentration (IC50) - Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. - - Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. - Bjoern Peters; Randi Vita - wikipedia - half maximal inhibitory concentration (IC50) - - - - - - - - - - - - - - + + + + + + + + + - epitope specific immune intervention - - An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope - Person: Bjoern Peters, Randi Vita, Jason Greenbaum - epitope specific immune intervention + Lead structure mapping assay + PMID:2686708 + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Lead probe + RNA ontology + Lead structure mapping assay - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - epitope specific cytokine production by T cells - - A process of cytokine production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific cytokine production by T cells - - - - - - - - + + - - + - - - - - - - - - - - - - - + + + + + + + + + + + + + - - An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|ELISPOT - ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells - - - - - - - - + - + - - - - - - - - - - - - - - - - - - - + + + + - operator variation design - - A study design that assesses the operator performance and relation to data consistency and quality. - Person: Chris Stoeckert, Jie Zheng - MO_519 operator_variation_design - operator variation design + RNASE T2 structure mapping assay + PMID:6207483 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse T2 + RNA ontology + RNASE T2 structure mapping assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects IP-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|cytometric bead array - cytometric bead array assay measuring epitope specific IP-10 production by T cells + + + gene dosage assay + + An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. + Bjoern Peters + David Osumi Sutherland + gene dosage assay - + - - + + - - + + - comparative genome hybridization by array design - - A study design that detects genomic copy number variations using microarray technology. - Person: Chris Stoeckert, Jie Zheng - MO_856 comparative_genome_hybridization_design - comparative genome hybridization by array design + + + + + + + + + + + + + + + + + + Fe-BABE RNA structure mapping assay + PMID: 7862644 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Fe-BABE probe + RNA ontology + Fe-BABE RNA structure mapping assay - + - - + + + - - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|biological activity - assay measuring epitope specific interleukin-27 production by T cells - - - - - - - - - - A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. - Person: Chris Stoeckert, Jie Zheng - MO_454 in_vivo_design - in vivo design - - - - - - - - - genotyping by high throughput sequencing design - - A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. - Person: Chris Stoeckert, Jie Zheng - MO_560 genotyping_design - genotyping by high throughput sequencing design - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - epitope specific tolerance induction by T cells + + + + + + + + + + + + + RNASE U2 structure mapping assay + PMID:409999 - A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific tolerance induction by T cells + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse U2 + RNA ontology + RNASE U2 structure mapping assay - + - - + + - - + + - innate behavior design - - A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. - Person: Chris Stoeckert, Jie Zheng - MO_355 innate_behavior_design - innate behavior design + binding constant determination assay + Determination of KD value for an antibody binding a protein using a BIACORE assay. + + A binding assay where the specified output is a binding constant + Bjoern Peters + Jason Greenbaum + Randi Vita + IEDB + binding constant determination assay - + - - - - - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + - - - - A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells + + + + NMIA RNA structure mapping assay + PMID: 15796531 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe + Philippe Rocca-Serra + SHAPE mapping assay + single nucleotide resolution mapping assay using NMIA probe + RNA ontology + NMIA RNA structure mapping assay - + - - - SNP microarray - - A DNA microarray used to detect polymorphisms in DNA samples - Person: Helen Parkinson - EFO_0002703 SNP array - SNP microarray + + + + + + + + + + + + + + + + + + + + + + + + + + Terbium RNA structure mapping assay + PMID:10772868 + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Terbium probe + RNA ontology + Terbium RNA structure mapping assay - + - - + + - - + + - + + + + + + + + + + + feature extraction + + A planed process with objective of obtaining quantified values from an image. + PERSON: Jie Zheng + MO_928: feature_extraction + + feature extraction + + + + + + + + + + + - - - - - - - + + + + - cell component comparison design - - A study design that compares samples from different cell components. - Person: Chris Stoeckert, Jie Zheng - MO_1019 cell_component_comparison_design - cell component comparison design + + + + + + + + + + + + + + + + + + OH-radical structure mapping assay + PMID:2501870 + + A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe + Philippe Rocca-Serra + MOHCA assay + OH footprinting assay + single nucleotide resolution mapping assay using OH-radical probe + RNA ontology + OH-radical structure mapping assay - + - - + + + - - + - - - - - - - - - - - - - - + + + + + + + + + - - - - An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|ELISPOT - ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - - - - - - - - - - - - - - - - - - - epitope specific macrophage inflammatory protein-1 alpha production by T cells - - A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific macrophage inflammatory protein-1 alpha production by T cells - - - - - - - - - - - - - - - - - - - epitope specific T cell activation - - A process of T cell activation resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific T cell activation - - - - - - - - - - - - + - - - - - - - - - - - - - - + + + + + + + + + - - A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|biological activity - assay measuring epitope specific interleukin-10 production by T cells - - - - - - - - + + - - + - - - - - - - - - - - - - - + + + + + + + + + - - - - A cytometric bead array assay that detects transforming growth factor-beta production by T cells - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|cytometric bead array - cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells - - - - - - - - - ex vivo design - - A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. - Person: Chris Stoeckert, Jie Zheng - MO_808 ex_vivo_design - ex vivo design - - - - - - - - - - - - - + + - - epitope specific type IV hypersensitivity by T cells + + + + + + + + + + + + + RNASE T1 structure mapping assay + PMID:114514 - A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific type IV hypersensitivity by T cells + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using RNAse T1 + RNA ontology + RNASE T1 structure mapping assay - + - - + + - - + + - - - - - - - - - - - - + + - normalization testing design - - A study design that tests different normalization procedures. - Person: Chris Stoeckert, Jie Zheng - MO_729 normalization_testing_design - normalization testing design + array image acquisition + + An image creation process that generate an image from the array. + PERSON: Jie Zheng + array image acquisition + MO_929: image_acquisition + array image creation - + - + - + - - - - - - - - - - - - - - - - - + + - A flow cytometry assay that detects epitope specific perforin release by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - perforin release|intracellular staining - intracellular material detection assay measuring epitope specific perforin release + light emission device + A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) + + A device which has a function to emit light. + Person:Helen Parkinson + OBI + light emission device - + - + - + - - - - - - - - - - - - - - - - - + + - A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|bioassay - cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells + perturbation device + + A homogenizer is a perturbation device. + + A perturbation device is a device which is designed to perform a perturb function + Helen Parkinson + OBI Vancouver workshop 2010 + PERSON: Helen Parkinson + perturbation device - + - + - + - + - - - - - - - - - - - - - - + + + + + + + - A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-22 release|biological activity - assay measuring epitope specific interleukin-22 production by T cells + environmental control device + A growth chamber is an environmental control device. + + An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. + Helen Parkinson + OBI + environmental control device - + - - + + + - - + - - - - - - - - - - - - - - + + + + + + + + + - - - - A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-8 release|biological activity - assay measuring epitope specific interleukin-8 production by T cells - - - - - - - - - - - - - - - - - - - epitope specific chemokine (C-C motif) ligand 1 production by T cells - - A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific chemokine (C-C motif) ligand 1 production by T cells - - - - - - - - - - - - + - - - - - - - - - - - - - - + + + + + + + + + - - A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|bioassay - cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells - - - - - - - - + @@ -26954,10 +32316,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + @@ -26965,3563 +32327,2590 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin - ArrayExpress production team - EFO:0002764 - ChIP-chip by SNP array assay + + + + + + + + + + + + Nuclease S1 structure mapping assay + PMID:363143 + + A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. + Philippe Rocca-Serra + single nucleotide resolution mapping assay using Nuclease S1 + RNA ontology + Nuclease S1 structure mapping assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects RANTES production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|ELISA - ELISA measuring epitope specific RANTES production by T cells + + + specimen fixation function + e.g the function of a bar code reader used to read slide bar codes + + a function that allows specific identification of individual speciment from one another. + EAGLE-I + specimen fixation function - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-1 beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells + + + obsolete_specimen fixation function + + A specimen fixation function is a function that holds or fastens an entity in a fixed position. + EAGLE-I + + obsolete_specimen fixation function + true - + - - + + - - + + + + + + + + + - genetic population background information - genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information - - a genetic characteristics information which is a part of genotype information that identifies the population of organisms - proposed and discussed on San Diego OBI workshop, March 2011 - Group: OBI group - Group: OBI group - genetic population background information - - - - - - - - - - + + - environmental history design - - A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. - Person: Chris Stoeckert, Jie Zheng - MO_698 environmental_history_design - environmental history design + + + + + + + + + + + + Ruthenium structure mapping assay + PMID:3016894 + + A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe + Philippe Rocca-Serra + RNA Ontology + Ruthenium structure mapping assay - + - - - - - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + - - - - An enzyme-linked immunospot assay that detects interleukin-6 production by T cells - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-6 production by T cells + + + + inline probing RNA structure mapping assay + PMID:10573122 and PMID: 18369975 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity + Philippe Rocca-Serra + RNA ontology + inline probing RNA structure mapping assay - + - - - - - - - - - - - - - - - - - - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. - IEDB - IEDB - antibody help|biological activity - biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response + + + current amplification function + + A current amplification function is an amplification function that increases the amplitude of a current. + EAGLE-I + current amplification function - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|surface plasmon resonance (SPR)|nM - plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex + + + stabilization function + + + A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity. + EAGLE-I + isolation function + stabilization function - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|biological activity - assay measuring epitope specific interleukin-5 production by T cells + + + pump function + + a transfer unction where the transfer requires work to move the entity, often against a gradient. + EAGLE-I + pump function - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|ELISA - ELISA measuring epitope specific transforming growth factor-beta production by T cells + + + cell transfer function + A cell harvester has a cell transfer function. + + is a transfer function that displaces cells from one place to another + EAGLE-I + cell transfer function - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects RANTES production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|biological activity - assay measuring epitope specific RANTES production by T cells + + + + + + + + + + + + + + + angiograph + + A device that records the patterns of pulse waves inside blood vessels. + PERSON: Erik Segerdell + http://medical-dictionary.thefreedictionary.com/angiograph + angiograph - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|biological activity - assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells + + + + + + + + + capillary blotter + + A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed. + PERSON: Erik Segerdell + http://www.biometra.de/ + capillary blotter - + - - - epigenetic modification identification objective + + + + + + + + + + + + + + + bioreactor - A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. - Chris Stoeckert, Jie Zheng - Person: Chris Stoeckert - epigenetic modification identification objective + A device or system that supports a biologically active environment. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Bioreactor + bioreactor - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + + pH meter - A transcription profiling by array assay that uses a tiling path array. - James Malone - EFO:0002769 - transcription profiling by tiling array assay + A device that is used to measure the pH (acidity or alkalinity) of a liquid. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/PH_meter + pH meter - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-22 release|ELISA - ELISA measuring epitope specific interleukin-22 production by T cells + + + + + + + + + digital camera + + An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Digital_camera + digital camera - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|biological activity - assay measuring epitope specific interleukin-21 production by T cells + + + + + + + + + chip spotting device + + A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray. + PERSON: Erik Segerdell + United States Patent 7416705 + chip spotting device - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-9 release|ELISA - ELISA measuring epitope specific interleukin-9 production by T cells + + + RNA extraction/purification instrument + + A device that is used to isolate and collect RNA for subsequent molecular analysis. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + RNA extraction/purification instrument - + - - + + - - + + + + + + + + + DNA extract - A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - transcription profiling by high throughput sequencing design + The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. + Person: Jie Zheng + Group: UPenn group + DNA extract - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A flow cytometry assay that detects interleukin-6 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells + + + two-photon laser/detector + + A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy + two-photon laser/detector - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|bioassay - cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells - + + + + + + + + + electrophoresis system + + A device that moves charged particles through a medium by using an electric field induced by electrodes. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Category:Electrophoresis + electrophoresis system + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells + + + + + + + + + PET synthesizer + + A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + PET synthesizer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|cytometric bead array - cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells + + + + + + + + + spinning-disk confocal microscope + + A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Nipkow_disk + spinning-disk confocal microscope - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|ELISA - ELISA measuring epitope specific interleukin-23 production by T cells + + + DNA synthesizer + + An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. + PERSON: Erik Segerdell + http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers + DNA synthesizer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - perforin release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release + + + high performance liquid chromatography instrument + + A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/High_performance_liquid_chromatography + high performance liquid chromatography instrument - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|ELISA - ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + + + + + + + + microplate reader + + A measurement device that detects biological, chemical or physical events of samples in microtiter plates. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Plate_reader + microplate reader - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + + ELISA microplate reader - A genotyping assay that uses a high througput sequencer - James Malone - EFO:0002771 - genotyping by high throughput sequencing assay + A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). + PERSON: Erik Segerdell + PERSON: Erik Segerdell + ELISA microplate reader - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + spot cutter - An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin - Bjoern Petesr - James Malone - ChIP-on-chip assay - url:http://en.wikipedia.org/wiki/ChIP-on-chip - ChIP-chip assay + A robotic device that is used to excise spots from gels. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + spot cutter - + - - - - - - - - - - - - - epitope specific T cell tolerance induction - - A process of T cell tolerance induction resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific T cell tolerance induction + + + + + + + + + + + + + + + microwave synthesis system + + A device that is used to apply microwave irradiation to chemical reactions. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Microwave_chemistry + microwave synthesis system - + - - - - An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - - - T cell degranulation by intracellular staining - obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation - true + + + + + + + + + densitometer + + A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Densitometer + densitometer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|biological activity - assay measuring epitope specific interleukin-13 production by T cells + + + + + + + + + + + + + + + automatic staining machine + + A device that is used to automatically stain tissue sections on slides or tissue specimens. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + automatic staining machine - + - - + + - - + + - - - - - - - - - - - - + + - array platform variation design + automatic tissue processor - A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. - Person: Chris Stoeckert, Jie Zheng - MO_899 array_platform_variation_design - array platform variation design + A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. + PERSON: Erik Segerdell + United States Patent 3762362 + automatic tissue processor - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-9 release|biological activity - assay measuring interleukin-9 production by T cells + + + + + + + + + stereo microscope + + An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope + stereo microscope - + - - - - - - - - - - - - - epitope specific interleukin-3 production by T cells - - A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-3 production by T cells + + + top loading balance + + A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + top loading balance - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells + + + + + + + + + perfusion station + + A device or system in which perfusion units are integrated. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + perfusion station - + - - - - - - - - - - - - - epitope specific lymphotoxin A production by T cells - - A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific lymphotoxin A production by T cells + + + + + + + + + + + + + + + SPECT scanner + + A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography + SPECT scanner - + - - - - - - - - - - - - - epitope specific interleukin-1 alpha production by T cells - - A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-1 alpha production by T cells + + + + + + + + + + + + + + + + + + + array manufacturer role + + a manufacturer role which is played by the person or organization that manufactured the array + PERSON: Chris Stoeckert, Jie Zheng + MO_695 array_manufacturer + array manufacturer role - + - - + + - - + + + scintillation counter + + A device that is used to measure ionizing radiation. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Scintillation_counter + scintillation counter + + + + + + + + - - + + - ChIP-seq design + programmable array microscope - A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. - Person: Chris Stoeckert, Jie Zheng - http://en.wikipedia.org/wiki/Chip-Sequencing - ChIP-seq design + A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. + PERSON: Erik Segerdell + Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8 + programmable array microscope - + - - + + - - + + + + + + + + + + + + + + - translational bias design + cryostat - A study design that characterizes the association of transcripts and translation machinery. - Person: Chris Stoeckert, Jie Zheng - MO_939 translational_bias_design - translational bias design + A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Cryostat + cryostat - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|ELISA - ELISA measuring epitope specific interleukin-3 production by T cells + + + + + + + + + microtome knife maker + + A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + microtome knife maker - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|ELISA - ELISA measuring epitope specific interleukin-1 alpha production by T cells + + + + + + + + + cryofixation device + + A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Cryofixation + cryofixation device - + - - - - - - - - - - - - - epitope specific interleukin-27 production by T cells - - A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-27 production by T cells + + + + + + + + + + + + + + + hybridization oven + + A device that creates an appropriate environment for nucleic acid hybridization. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + hybridization oven - + - - - - - - - - - - - - - - - - - - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - T cell help|biological activity - biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response + + + + + + + + + + + + + + + + + + + + + incubator shaker + + An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). + PERSON: Erik Segerdell + PERSON: Erik Segerdell + incubator shaker - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|biological activity - assay measuring epitope specific transforming growth factor-beta production by T cells + + + + + + + + + + + + + + + small-animal image acquisition device + + A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + small-animal image acquisition device - + - - - FWER adjusted p-value - http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html - - A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests - PERS:Philippe Rocca-Serra - adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) - FWER adjusted p-value + + + + + + + + + + + + + + + infrared image acquisition device + + An image acquisition device that is responsive to an infrared emissive target within a given field of view. + PERSON: Erik Segerdell + United States Patent 4107530 + infrared image acquisition device - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + + confocal microscope - A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology - ArrayExpress production team - Helen Parkinson - James Malone - EFO:0002761 - DNA methylation profiling by high throughput sequencing assay + A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Confocal_microscopy + confocal microscope - + - - - - - - - - - - - - - epitope specific transforming growth factor-beta production by T cells - - A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific transforming growth factor-beta production by T cells + + + + + + + + + patch clamp device + + A device used in electrophysiology that allows the study of single or multiple ion channels in cells. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Patch_clamp + patch clamp device - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells + + + + + + + + + + + + + + + gel imaging system + + A device that is used to acquire images of laboratory gels. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + gel imaging system - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - degranulation|biological activity - assay measuring epitope specific cytotoxic T cell degranulation + + + + + + + + + protein separation apparatus + + A device that is used for the separation of proteins. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + protein separation apparatus - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TGFb release|bioassay - cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells + + + multichannel electronic pipette + + A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations. + PERSON: Erik Segerdell + http://www.faqs.org/patents/app/20090196797 + multichannel electronic pipette - + - - + + - - - - - - - + + + vitrification apparatus - An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. - James Malone - transcription profiling by high throughput sequencing - EFO:0002770 - RNA-seq assay + A device that is used to effect the transition of a substance into a glass. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Glass_transition + vitrification apparatus - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|ELISPOT - ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - - - + - + + + + + + + + + + + + + + + radiography instrument + + An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Medical_radiography + radiography instrument + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|bioassay - cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells + + + + + + + + + + + + + + + + + + radiation measurement device + + A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + radiation measurement device - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + lyophilizer - A genotyping assay that uses an array - ArrayExpress production team - EFO:0002767 - genotyping by array assay + A device that is used to freeze dry material. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Freeze_drying + lyophilizer - + - - - - - - - - - - - - - epitope specific interleukin-16 production by T cells - - A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-16 production by T cells + + + tandem mass spectrometer + + A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. + PERSON: Erik Segerdell + http://goldbook.iupac.org/T06250.html + tandem mass spectrometer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|biological activity - assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + + + + + + + + + microhardness tester + + A hardness testing device that is used in light-optical microscopes. + PERSON: Erik Segerdell + United States Patent 4611487 + microhardness tester - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells + + + multimode microplate reader + + A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + multimode microplate reader - + - - - - - - - - - DNA methylation profiling by array design + + + mechanical balance - A study design in which the methylation state of DNA is determined and is compared between samples using array technology. - Person: Chris Stoeckert, Jie Zheng - GROUP: ArrayExpress production team - DNA methylation profiling by array design + A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). + PERSON: Erik Segerdell + http://www.britannica.com/EBchecked/topic/49765/balance + mechanical balance - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-22 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells + + + computer cluster + + A group of linked computers, working together closely so that in many respects they form a single computer. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Cluster_(computing) + computer cluster - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|biological activity - assay measuring epitope specific interleukin-16 production by T cells + + + + + + + + + microtome knife sharpener + + A device that is used to sharpen knives used in microtomy. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + microtome knife sharpener - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects IP-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|ELISA - ELISA measuring epitope specific IP-10 production by T cells + + + + + + + + + plate shaker + + A device that provides shaking motion for microplates. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + plate shaker - + - - + + - - + + + coagulation analyzer - An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. - James Malone - EFO:0001033 - translation profiling assay + A device for automatically analyzing blood coagulation in a clinical laboratory. + PERSON: Erik Segerdell + United States Patent 5439646 + coagulation analyzer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|ELISA - ELISA measuring epitope specific interleukin-15 production by T cells + + + + + + + + + laser capture microdissection microscope + + A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. + PERSON: Erik Segerdell + http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine + laser capture microdissection microscope - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-12 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-12 production by T cells + + + + + + + + + liquid extraction robot + + A liquid handling device that provides automatic liquid extraction. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + liquid extraction robot - + - - - in vitro design + + + + + + + + + + + + + + + ultrasound machine - A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. - Person: Chris Stoeckert, Jie Zheng - MO_347 in_vitro_design - in vitro design + A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Sonography + ultrasound machine - + - - + + - - + + + + + + + + - RNAi profiling by array design + immunoblot scanner - A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - RNAi profiling by array design + A device that is used for the imaging of immunoblots. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + immunoblot scanner - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - lymphotoxin A/TNFb release|ELISA - ELISA measuring epitope specific lymphotoxin A production by T cells + + + microcentrifuge + + A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Laboratory_centrifuge + microcentrifuge - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-5 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-5 production by T cells + + + electronic repeater pipette + + A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. + PERSON: Erik Segerdell + http://www.faqs.org/patents/app/20090196797 + electronic repeater pipette - + - - + + + electron paramagnetic resonance spectrometer + + An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance + electron paramagnetic resonance spectrometer + + + + + + + + - - + + - transcription profiling by array design + rocker - A study design that identifies forms and abundance of transcripts in the genome using microarray technology. - Person: Chris Stoeckert, Jie Zheng - MO_533 transcript_identification_design - transcription profiling by array design + A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). + PERSON: Erik Segerdell + PERSON: Erik Segerdell + rocker - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells + + + analytical balance + + A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Weighing_scale + analytical balance - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|biological activity - assay measuring epitope specific interleukin-15 production by T cells + + + + + + + + + scanning force microscope + + A microscope that forms images of surfaces using a physical probe that scans the specimen. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Scanning_probe_microscopy + scanning force microscope - + - - + + + pulsed-field gel electrophoresis system + + A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis + pulsed-field gel electrophoresis system + + + + + + + + - - + + + tissue embedding station + + A device that is used to perform paraffin embedding of tissue specimens. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + tissue embedding station + + + + + + + + - - - - - - - - - - - - + + - disease state design + nucleic acid sequencer - A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. - Person: Chris Stoeckert, Jie Zheng - MO_902 disease_state_design - disease state design + An device that is used to determine the order of nucleotides in nucleic acid sequences. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + nucleic acid sequencer - + - - - wild type organism genotype information - C57BL/6J wild type + + + + + + + + + + + + + + + bead array reader - a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. - proposed and discussed on San Diego OBI workshop, March 2011 - Group: OBI group - Group: OBI group - wild type organism genotype information + A device that is used to acquire and image bead array data. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + bead array reader - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|biological activity - assay measuring epitope specific interleukin-17 production by T cells + + + real-time PCR machine + + An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction + real-time PCR machine - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-17 production by T cells + + + + + + + + + + + + + + + + + + + + + paraffin oven + + A device that is used for the warming of paraffin embedding medium. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + paraffin oven - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-10 production by T cells. - IEDB - IEDB - IL-10 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-10 production by T cells + + + + + + + + + + + + + + + + + + + + + autoclave + + A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents. + PERSON: Erik Segerdell + J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave + autoclave - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells + + + + + + + + + microplate washer + + A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? + PERSON: Erik Segerdell + http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037 + microplate washer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A flow cytometry assay that detects interleukin-5 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells + + + + + + + + + nucleic acid extraction/purification instrument + + A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + nucleic acid extraction/purification instrument - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-2 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-2 production by T cells + + + ELISA microplate washer + + A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). + PERSON: Erik Segerdell + PERSON: Erik Segerdell + ELISA microplate washer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|bioassay - cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells + + + + + + + + + vacuum manifold + + A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + vacuum manifold - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|ELISA - ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + + DNA extraction/purification instrument + + A device that is used to isolate and collect DNA for subsequent molecular analysis. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/DNA_extraction + DNA extraction/purification instrument - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|ICS - intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + + + + + + + + + + + + + + + multichannel pipette + + A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + multichannel pipette - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + cell harvester + + A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? + PERSON: Erik Segerdell + PERSON: Erik Segerdell + cell harvester + + + + + + + + + portable fluorometer + + A compact fluorometer that can be carried or moved with ease. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + portable fluorometer + + + + + + + + + gel electrophoresis system + + An electrophoresis system in which an electric field is applied to a gel matrix + PERSON: Erik Segerdell + https://en.wikipedia.org/wiki/Gel_electrophoresis + gel electrophoresis system + + + + + + + + - - + + + diffractometer - An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. - James Malone - EFO:0001030 - RNAi profiling by array assay + A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Diffractometer + diffractometer - + - - + + - - - - - - - - - - - - + + + + - genotype information - Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information + microdissection instrument - a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. - discussed on San Diego OBI workshop, March 2011 - Group: OBI group - Group: OBI group - genotype information + A device that is used for the dissection of tissues under magnification. + PERSON: Erik Segerdell + http://medical-dictionary.thefreedictionary.com/microdissection + microdissection instrument - + - - + + - - - - - - - - - - - - + + - RNA stability design + micropipette puller - A study design that examines the stability and/or decay of RNA transcripts. - Person: Chris Stoeckert, Jie Zheng - MO_553 RNA_stability_design - RNA stability design + A device that is used to fabricate glass micropipettes. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Micropipette + micropipette puller - + - - - tiling microarray + + + + + + + + + laser scanning confocal microscope - A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. - Person: Helen Parkinson - genome tiling array - EFO_0002704: tiling array - tiling microarray + A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy + laser scanning confocal microscope - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects IP-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|biological activity - assay measuring epitope specific IP-10 production by T cells + + + + + + + + + digital microscope + + A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Digital_microscope + digital microscope - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A flow cytometry assay that detects interleukin-13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells + + + + + + + + + + + + + + + freeze substitution system + + A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins. + PERSON: Erik Segerdell + doi:10.1017/S143192760707866X + freeze substitution system - + - - + + - - + + - - - - - - - - - - - - + + - species comparison design + micropipette - A study design that assays differences between distinct species. - Person: Chris Stoeckert, Jie Zheng - MO_675 species_design - species comparison design + A microinjection device that is used to measure very small volumes of liquids. + PERSON: Erik Segerdell + http://www.answers.com/topic/micropipette + micropipette - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|x-ray crystallography|angstroms - X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex + + + + + + + + + voltage clamp device + + A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Voltage_clamp + voltage clamp device - + - - + + - - + + + + + + + + + + + + + + - transcription profiling by RT-PCR design + vacuum oven - A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - transcription profiling by RT-PCR design + A device that heats materials in a vacuum. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + vacuum oven - + - - - - - - - - - - - - - epitope specific T cell enhancement of B cell mediated immune response - - A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific T cell enhancement of B cell mediated immune response + + + + + + + + + slide warmer + + A device that is used to heat microscope slides. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + slide warmer - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|ELISA - ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + + + capillary electrophoresis instrument + + An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Capillary_electrophoresis + capillary electrophoresis instrument - + - - - - - - - - - - - - - epitope specific interleukin-21 production by T cells - - A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-21 production by T cells + + + + + + + + + denaturing high-performance liquid chromatography instrument + + A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis. + PERSON: Erik Segerdell + doi:10.1385/1-59259-850-1:173 + denaturing high-performance liquid chromatography instrument - + - - + + + agarose gel electrophoresis system + + A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis + agarose gel electrophoresis system + + + + + + + + - - + + - - - - - - - + + - A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - T cell- APC binding|binding assay - flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex + balance + + A measuring instrument that is used to determine the weight or mass of an object. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Weighing_scale + balance - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + + surface plasmon resonance instrument + + A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles. + PERSON: Erik Segerdell + http://en.wikipedia.org/wiki/Surface_plasmon_resonance + surface plasmon resonance instrument + + + + + + + + - - - - - - - - - - - - + + + protein sequencer + + An device that is used to determine the order of amino acids in protein sequences. + PERSON: Erik Segerdell + PERSON: Erik Segerdell + protein sequencer + + + + + + + + - - + + + X-ray source - An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. - James Malone - EFO:0002765 - proteomic profiling by array assay + A device that is used to generate X-rays. + PERSON: Erik Segerdell + x-ray generator + http://en.wikipedia.org/wiki/X-ray_generator + X-ray source - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|bioassay - cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells + + + liquid chromatography instrument + + A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated + PERSON: Matthew Brush + PERSON: Matthew Brush + liquid chromatography instrument - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - granzyme B release|ELISPOT - ELISPOT assay measuring epitope specific granzyme B release by T cells + + + spike-in quality control role + + a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes + PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter + MO_937 spike_quality_control + spike-in quality control role - + - - + + - - + + - microRNA profiling by array design + individual organism identifier - A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - microRNA profiling by array design + a CRID symbol used to distinguish one individual organism from another. + PERSON: Chris Stoeckert, Jie Zheng + MO_169 Individual + individual organism identifier - + - - + + + + + + + + + dye swap quality control role + + a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes + PERSON: Chris Stoeckert, Jie Zheng + MO_524 dye_swap_quality_control + dye swap quality control role + + + + + + + + + - - + - - + + + + + - - - - - - - + + - - An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - tolerance|in vivo assay - in vivo assay measuring T cell epitope specific tolerance induction + + + + + + + + labeled nucleic acid extract + + a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. + Person: Jie Zheng + labeled extract + MO_221 labeledExtract + labeled extract + labeled nucleic acid extract - + - + + + binding constant + The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes". + + A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed. + 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. + PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum + binding constant + + + + + + + - + + + + + - - - - - - - - - - - + - A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells. - IEDB - IEDB - CCL5/RANTES release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells + 3D structure determination of bound molecular complex assay + Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. + + A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration. + IEDB + IEDB + 3D structure determination of bound molecular complex assay - + - - + + + + + + + + + + + + + + + + + + + + binding assay + Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. + + An assay with the objective to characterize the disposition of two or more material entities to form a complex. + Bjoern Peters + Jason Greenbaum + Randi Vita + binding assay + + + + + + + + + - + + + + - - - - - - - - - - - - - - - - + - - A cytometric bead array assay that detects interleukin-4 production by T cells - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-4 production by T cells + + + + + + + + cell culture expansion + + a process that results in the increase of cell numbers + including grow of yeast and bacteria + PERSON: Chris Stoeckert, Jie Zheng + MO_758 grow + BP: +add it as subclass of 'cell culturing' +JZ: +No 'cell culturing' in OBI +Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process. + cell culture expansion - + - + + + gene knock out + + a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. + PERSON: Chris Stoeckert, Jie Zheng + MO_771 gene_knock_out + gene knock out + + + + + + + + + gene knock in + + a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. + PERSON: Chris Stoeckert, Jie Zheng + MO_437 gene_knock_in + WEB: http://en.wikipedia.org/wiki/Gene_Knock-in + gene knock in + + + + + + + + + chromosomal substitution + + A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'. + PERSON: Chris Stoeckert, Jie Zheng + MO_995 chromosomal_substitution + chromosomal substitution + + + + + + + - - - - - + + + + + - - - - - - - - - - - - + + - - - + + + - A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - lymphotoxin A/TNFb release|biological activity - assay measuring epitope specific lymphotoxin A production by T cells + + genetically modified material + + a material entity, organism or cell, that is the output of a genetic transformation process. + PERSON: Jie Zheng + GROUP: OBI + term is proposed by BP on Oct 25, 2010 dev call + genetically modified material - + - - + + + + + + + + - + + + + + + - - - - - - - - - - - - + + - organism development design + transfection - A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. - Person: Chris Stoeckert, Jie Zheng - MO_892 development_or_differentiation_design - organism development design + a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell + PERSON: Chris Stoeckert, Jie Zheng + MO_366 transfection + transfection - + - - - - - - - - - family history design + + + genetic transformation objective - A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. - Person: Chris Stoeckert, Jie Zheng - MO_544 family_history_design - family history design + a material transformation objective aims to create genetically modified organism or cell + Person: Jie Zheng + Person: Jie Zheng + suggested to be added by BP and AR during Oct 25, 2010 dev call + genetic transformation objective - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. - IEDB - IEDB - CXCL9/MIG release|ELISA - ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + + + induced mutagenesis + + A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation. + Label and definition were clarified as per https://github.com/obi-ontology/obi/issues/1366 + PERSON: Chris Stoeckert, Jie Zheng + MO_564 induced_mutation + induced mutagenesis - + - - - transcription profiling identification objective + + + 3D structural organization datum + The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. + + A measurement datum that describes the structural orientation of a material entity in 3D space. + PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters + 3D structural organization datum + + + + + + + + + age since planting measurement datum - A molecular feature identification objective that aims to characterize the abundance of transcripts - Person: Chris Stoeckert, Jie Zheng - Group: Penn Group - transcription profiling identification objective + An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. + PERSON:Chris Stoeckert, Jie Zheng + MO_495 planting + Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. +Term proposed by Bjoern on Nov 8, 2010 dev call +Supported by Alan on Nov 15, 2010 dev call + age since planting measurement datum - + - - + + + age since hatching measurement datum + + An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. + PERSON:Chris Stoeckert, Jie Zheng + MO_745 hatching + age since hatching measurement datum + + + + + + + + @@ -30530,10 +34919,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + @@ -30541,87 +34930,215 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + + + + + + + + + + + + + + + + + + age determination assay - A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology - James Malone - EFO:0002759 - DNA methylation profiling by array assay + An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). + This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. + Alan Ruttenberg + age measurement assay + OBI group + age determination assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|biological activity - assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + + age since egg laying measurement datum + + An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. + PERSON:Chris Stoeckert, Jie Zheng + MO_767 egg laying + age since egg laying measurement datum - + - - - - - - - - - - - - - epitope specific granulocyte colony stimulating factor production by T cells - - A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific granulocyte colony stimulating factor production by T cells + + + assay validation objective + + an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results + PERSON: Chris Stoeckert, Jie Zheng + GROUP: Penn Group + assay validation objective - + - - + + + age since germination measurement datum + + An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. + Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. + PERSON:Chris Stoeckert, Jie Zheng + MO_590 germination + age since germination measurement datum + + + + + + + + + validation by reverse transcription PCR design + + a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results + PERSON: Chris Stoeckert, Jie Zheng + MO_986 reverse_transcription_PCR_quality_control + validation by reverse transcription PCR design + + + + + + + + + age since eclosion measurement datum + + An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. + PERSON:Chris Stoeckert, Jie Zheng + MO_876 eclosion + age since eclosion measurement datum + + + + + + + + + age since sowing measurement datum + + An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. + PERSON:Chris Stoeckert, Jie Zheng + MO_748 sowing + age since sowing measurement datum + + + + + + + + + age since coitus measurement datum + + An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. + PERSON:Chris Stoeckert, Jie Zheng + MO_783 coitus + age since coitus measurement datum + + + + + + + + + validation by real time PCR design + + a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results + PERSON: Chris Stoeckert, Jie Zheng + MO_434 real_time_PCR_quality_control + validation by real time PCR design + + + + + + + + + + + + + + + age measurement datum + + A time measurement datum that is the result of measurement of age of an organism + note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. +life of bearer doesn't imply organism +this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature +age as a quality is dubious; we plan to revisit +stages in development are currently handled with controlled vocabulary, such as 2-somite stage + PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng + MO_178 Age + In MageTab file, we use +initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) +Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class + discussed on Nov 15, dev call +All subtype will be defined by textual definition now. + age measurement datum + + + + + + + + + age since fertilization measurement datum + + An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. + Definition of fertilization comes from GO. + PERSON:Chris Stoeckert, Jie Zheng + MO_701 fertilization + age since fertilization measurement datum + + + + + + + + + age since birth measurement datum + + An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. + PERSON:Chris Stoeckert, Jie Zheng + MO_710 birth + age since birth measurement datum + + + + + + + + @@ -30630,10 +35147,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - - + + @@ -30641,55 +35158,37 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - + - - + + - - - - + + + + + + - - - - - - - - - - - + - + @@ -30698,536 +35197,570 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + + reverse transcription polymerase chain reaction assay + + An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. + Chris Stoeckert + Jie Zheng + Penn Group + reverse transcription polymerase chain reaction assay + + + + + + + + - - + + + half life datum (t 1/2) - An assay that analyses the microRNA component of the transcriptome using a microRNA array. - James Malone - EFO:0000753 - microRNA profiling by array assay + The time it takes for 50% of a class of stochastic processes to occur. + Bjoern Peters + t 1/2 + Bjoern Peters + half life datum (t 1/2) - + - - - quality control testing design + + + dose response curve - A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. - Person: Chris Stoeckert, Jie Zheng - MO_981 quality_control_testing_design - quality control testing design + A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. + Bjoern Peters; Randi Vita + dose response curve - + - - + + + + + + + + + + + + + + + + + + + + + + + + service + providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony + + A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. + Carlo; Matt + OBI workshop San Diego 2011 + service + + + + + + + + + + + - + - - + + - clinical history design - - A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. - Person: Chris Stoeckert, Jie Zheng - MO_832 clinical_history_design - clinical history design + passive immunization + Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. +Transferring epitope specific T cells from one mouse into another. + + The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. + PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum + adoptive transfer + passive immunization - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells + + + selective organism creation objective + + an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. + PERSON: Chris Stoeckert, Jie Zheng + WEB: wikipedia +http://en.wikipedia.org/wiki/Cultivar +http://en.wikipedia.org/wiki/Ecotype +http://en.wikipedia.org/wiki/Strain_%28biology%29 + selective organism creation objective - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|bioassay - cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + + + Individual epitope immunization in vivo + Injection of a peptide T cell epitope into a mouse + + An immunization in which an individual epitope is administered into a host organism. + 3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here. + PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita + Individual epitope immunization in vivo - + - + - - - - + + + - + - + - - + + - - - - - - A flow cytometry assay that detects interleukin-21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells - - - - - - - - - - - - - - - + + + + + + + + + - + - - + + - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - - - - - - - - - - - - - - - + - + - - + + - + + + + + + + + + + + + + - - - - An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|ELISA - ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells - - - - - - - - - - - - - - - - - - - - - - + - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL4/MIP-1b release|biological activity - assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + RNA sequencing assay + + An assay that determines the sequence of an RNA molecule. + Bjoern Peters + Bjoern Peters + RNA sequencing assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|ELISA - ELISA measuring epitope specific interleukin-21 production by T cells + + + efficacy of epitope intervention experiment + + An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism. + Bjoern Peters + efficacy of in vivo intervention + efficacy of epitope intervention experiment - + - - - - - - - - - - - - - - - - - - An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - type IV hypersensitivity (DTH)|in vivo skin test - in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity + + + epitope protection from infectious challenge experiment + + An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. + Bjoern Peters + protection from infectious challenge + epitope protection from infectious challenge experiment - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-13 production by T cells + + + + + + + + + + + + + + + half maximal effective concentration (EC50) + Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. + + half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. + + Bjoern Peters; Randi Vita + wikipedia + half maximal effective concentration (EC50) - + - + - + - - - - - - - - - - - - - - - - - + + - A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells + binding datum + + A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. + Bjoern Peters; Randi Vita + binding datum - + - + + + negative binding datum + + A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. + negative binding datum + + + + + + + + + epitope protection from tumor challenge experiment + + An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. + Bjoern Peters + protection from tumor challenge + epitope protection from tumor challenge experiment + + + + + + + + + epitope protection experiment + + An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. + Bjoern Peters + protection from challenge + epitope protection experiment + + + + + + + - + - - + + + + + + + + + + + + - epitope specific tumor necrosis factor superfamily cytokine production by T cells - - A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific tumor necrosis factor superfamily cytokine production by T cells + selectively maintained organism + + An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms + Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert + cultivar + ecotype + strain + MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar + selectively maintained organism - + - - + + + epitope protection from infectious challenge experiment based on pathogen burden + + An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. + Bjoern Peters + burden after infectious challenge + epitope protection from infectious challenge experiment based on pathogen burden + + + + + + + + - - - - - - + + + - + - + + + + infectious agent detection assay + Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus. + + An assay that measures the presence or amount of an infectious agent in an evaluant + Bjoern Peters + Jason Greenbaum + Randi Vita + Richard Scheuermann + infectious agent detection assay + + + + + + + + + epitope disease exacerbation experiment + + An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. + Bjoern Peters + exacerbation assay + epitope disease exacerbation experiment + + + + + + + + + epitope protection experiment based on survival + + An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. + Bjoern Peters + host survival after challenge + epitope protection experiment based on survival + + + + + + + + + epitope treatment experiment + + An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. + Bjoern Peters + decreased disease symptoms after treatment + epitope treatment experiment + + + + + + + + + + + + + + + + + + + + + half maximal inhibitory concentration (IC50) + Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. + + Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. + Bjoern Peters; Randi Vita + wikipedia + half maximal inhibitory concentration (IC50) + + + + + + + + + + + + + + - allele information - genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information + epitope specific immune intervention - a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. - discussed on San Diego OBI workshop, March 2011 - Person: Chris Stoeckert, Jie Zheng - MO_58 Allele - allele information + An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope + Person: Bjoern Peters, Randi Vita, Jason Greenbaum + epitope specific immune intervention - + - + - + - - - - - - - - - - - - - - - - - + + - A cytometric bead array assay that detects tumor necrosis factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|cytometric bead array - cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells + epitope specific cytokine production by T cells + + A process of cytokine production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific cytokine production by T cells - + - + @@ -31240,7 +35773,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31254,60 +35787,64 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - An enzyme-linked immunospot assay that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-17 production by T cells + ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells + + An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|ELISPOT + ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells - + - - - - - - - - + + + + + + + + + - + - - + + - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells + + + + + + operator variation design + + A study design that assesses the operator performance and relation to data consistency and quality. + Person: Chris Stoeckert, Jie Zheng + MO_519 operator_variation_design + operator variation design - + - + - + @@ -31316,7 +35853,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31330,59 +35867,44 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + cytometric bead array assay measuring epitope specific IP-10 production by T cells + + A cytometric bead array assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|cytometric bead array + cytometric bead array assay measuring epitope specific IP-10 production by T cells - + - - - - - - - - + + - - - - - - - - - - - + - post-transcriptional modification design + comparative genome hybridization by array design - A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. - post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases - Person: Chris Stoeckert, Jie Zheng - MO_392 cellular_modification_design - post-transcriptional modification design + A study design that detects genomic copy number variations using microarray technology. + Person: Chris Stoeckert, Jie Zheng + MO_856 comparative_genome_hybridization_design + comparative genome hybridization by array design - + - + - + @@ -31391,7 +35913,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31405,103 +35927,52 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-8 release|ELISA - ELISA measuring epitope specific interleukin-8 production by T cells + assay measuring epitope specific interleukin-27 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|biological activity + assay measuring epitope specific interleukin-27 production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-6 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-6 production by T cells + + + in vivo design + + A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. + Person: Chris Stoeckert, Jie Zheng + MO_454 in_vivo_design + in vivo design - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + genotyping by high throughput sequencing design - A transcription profiling assay that uses reverse transcription PCR (RT-PCR). - Anna Farne - EFO:0002943 - transcription profiling by RT-PCR assay + A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. + Person: Chris Stoeckert, Jie Zheng + MO_560 genotyping_design + genotyping by high throughput sequencing design - + - + - + @@ -31509,24 +35980,44 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific chemokine (C-C motif) ligand 4 production by T cells + epitope specific tolerance induction by T cells - A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific chemokine (C-C motif) ligand 4 production by T cells + A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific tolerance induction by T cells - + - + + + + + + + + + innate behavior design + + A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. + Person: Chris Stoeckert, Jie Zheng + MO_355 innate_behavior_design + innate behavior design + + + + + + + - + @@ -31535,7 +36026,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31549,92 +36040,74 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|biological activity - assay measuring epitope specific interleukin-23 production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells - + - - - genetic alteration information + + + SNP microarray - a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. - proposed and discussed on San Diego OBI workshop, March 2011 - Group: OBI group - Group: OBI group - genetic alteration information + A DNA microarray used to detect polymorphisms in DNA samples + Person: Helen Parkinson + EFO_0002703 SNP array + SNP microarray - + - + + + + + + + - + - + - cellular process design + cell component comparison design - A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - Person: Chris Stoeckert, Jie Zheng - MO_810 cellular_process_design - cellular process design - - - - - - - - - - - - - - - - - - - epitope specific RANTES production by T cells - - A process of RANTES production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific RANTES production by T cells + A study design that compares samples from different cell components. + Person: Chris Stoeckert, Jie Zheng + MO_1019 cell_component_comparison_design + cell component comparison design - + - + - + @@ -31643,7 +36116,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31657,75 +36130,74 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells + ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + + An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|ELISPOT + ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - + - + - + - - - - - - - - - - - - - - - - - + + - A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|cytometric bead array - cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + epitope specific macrophage inflammatory protein-1 alpha production by T cells + + A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific macrophage inflammatory protein-1 alpha production by T cells - + - - - wild type allele information - - an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. - discussed on San Diego OBI workshop, March 2011 - Person: Chris Stoeckert, Jie Zheng - MO_605 genotype - wild type allele information + + + + + + + + + + + + + epitope specific T cell activation + + A process of T cell activation resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific T cell activation - + - + - + @@ -31734,7 +36206,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31748,47 +36220,78 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL4/MIP-1b release|ICS - intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + assay measuring epitope specific interleukin-10 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|biological activity + assay measuring epitope specific interleukin-10 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - epitope specific granzyme B production by T cells - - A process of granzyme B production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific granzyme B production by T cells + cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells + + A cytometric bead array assay that detects transforming growth factor-beta production by T cells + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|cytometric bead array + cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells - + - + + + ex vivo design + + A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. + Person: Chris Stoeckert, Jie Zheng + MO_808 ex_vivo_design + ex vivo design + + + + + + + - + @@ -31796,40 +36299,56 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-8 production by T cells + epitope specific type IV hypersensitivity by T cells - A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-8 production by T cells + A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific type IV hypersensitivity by T cells - + - + - + + + + + + + + + + + + + + + + + - injury design + normalization testing design - A study design in which the response of an organism(s) to injury or damage is studied. - Person: Chris Stoeckert, Jie Zheng - MO_726 injury_design - injury design + A study design that tests different normalization procedures. + Person: Chris Stoeckert, Jie Zheng + MO_729 normalization_testing_design + normalization testing design - + - + @@ -31842,7 +36361,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31856,70 +36375,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A flow cytometry assay that detects interleukin-3 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - organism status comparison design + intracellular material detection assay measuring epitope specific perforin release - A study design that compares samples from live and dead organisms. - Person: Chris Stoeckert, Jie Zheng - MO_841 organism_status_design - organism status comparison design + A flow cytometry assay that detects epitope specific perforin release by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + perforin release|intracellular staining + intracellular material detection assay measuring epitope specific perforin release - + - + - + @@ -31928,7 +36401,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31942,22 +36415,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL4/MIP-1b release|ELISA - ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells + + A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|bioassay + cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells - + - + - + @@ -31966,7 +36441,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -31980,18 +36455,20 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A cytometric bead array assay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|cytometric bead array - cytometric bead array assay measuring epitope specific interferon-gamma production by T cells + assay measuring epitope specific interleukin-22 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-22 release|biological activity + assay measuring epitope specific interleukin-22 production by T cells - + - + @@ -32004,7 +36481,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32018,22 +36495,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|biological activity - assay measuring epitope specific interleukin-18 production by T cells + assay measuring epitope specific interleukin-8 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-8 release|biological activity + assay measuring epitope specific interleukin-8 production by T cells - + - + - + @@ -32041,24 +36520,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - epitope specific interleukin-23 production by T cells + epitope specific chemokine (C-C motif) ligand 1 production by T cells - A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-23 production by T cells + A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific chemokine (C-C motif) ligand 1 production by T cells - + - + - + @@ -32067,7 +36546,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32081,22 +36560,62 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells + cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells + + A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|bioassay + cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + ChIP-chip by SNP array assay + + A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin + ArrayExpress production team + EFO:0002764 + ChIP-chip by SNP array assay + + + + + + + - + @@ -32105,7 +36624,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32119,22 +36638,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells + ELISA measuring epitope specific RANTES production by T cells + + An enzyme-linked immunosorbent assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|ELISA + ELISA measuring epitope specific RANTES production by T cells - + - + - + @@ -32143,7 +36664,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32157,22 +36678,66 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|bioassay - cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells + cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells + + A cytometric bead array assay that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells - + - + + + + + + + + + genetic population background information + genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information + + a genetic characteristics information which is a part of genotype information that identifies the population of organisms + proposed and discussed on San Diego OBI workshop, March 2011 + Group: OBI group + Group: OBI group + genetic population background information + + + + + + + + + + + + + + + environmental history design + + A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. + Person: Chris Stoeckert, Jie Zheng + MO_698 environmental_history_design + environmental history design + + + + + + + - + @@ -32181,7 +36746,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32195,57 +36760,127 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|ICS - intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + ELISPOT assay measuring epitope specific interleukin-6 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-6 production by T cells + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-6 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - epitope specific monocyte chemotactic protein-1 production by T cells - - A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific monocyte chemotactic protein-1 production by T cells + in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response + + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. + IEDB + IEDB + antibody help|in vivo assay + in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response - + - - - genotyping by array design + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex - A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. - Person: Chris Stoeckert, Jie Zheng - MO_560 genotyping_design - genotyping by array design + A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|surface plasmon resonance (SPR)|nM + plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex - + - + @@ -32258,7 +36893,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32272,22 +36907,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|biological activity - assay measuring epitope specific interleukin-1 alpha production by T cells + assay measuring epitope specific interleukin-5 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|biological activity + assay measuring epitope specific interleukin-5 production by T cells - + - + - + @@ -32296,7 +36933,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32310,18 +36947,20 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells + ELISA measuring epitope specific transforming growth factor-beta production by T cells + + An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|ELISA + ELISA measuring epitope specific transforming growth factor-beta production by T cells - + - + @@ -32334,7 +36973,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32348,18 +36987,20 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|biological activity - assay measuring epitope specific interferon-beta production by T cells + assay measuring epitope specific RANTES production by T cells + + A T cell epitope specific cytokine production assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|biological activity + assay measuring epitope specific RANTES production by T cells - + - + @@ -32372,7 +37013,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32386,49 +37027,35 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|biological activity - assay measuring epitope specific interleukin-12 production by T cells + assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells + + A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|biological activity + assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells - + - - - - - - - - - - - - - - - - - - - - A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - cytotoxicity|in vivo assay - in vivo assay measuring epitope specific T cell killing + + + epigenetic modification identification objective + + A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. + Chris Stoeckert, Jie Zheng + Person: Chris Stoeckert + epigenetic modification identification objective - + - - + + @@ -32440,7 +37067,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32448,105 +37075,108 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + transcription profiling by tiling array assay + + A transcription profiling by array assay that uses a tiling path array. + James Malone + EFO:0002769 + transcription profiling by tiling array assay + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + ELISA measuring epitope specific interleukin-22 production by T cells - An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. - James Malone - array CGH - EFO:0000749 - comparative genomic hybridization by array assay + An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-22 release|ELISA + ELISA measuring epitope specific interleukin-22 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - epitope specific cytotoxic T cell degranulation - - A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific cytotoxic T cell degranulation + assay measuring epitope specific interleukin-21 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|biological activity + assay measuring epitope specific interleukin-21 production by T cells - + - + - + @@ -32555,7 +37185,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32569,68 +37199,44 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells + ELISA measuring epitope specific interleukin-9 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-9 release|ELISA + ELISA measuring epitope specific interleukin-9 production by T cells - + - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - + - stimulus or stress design + transcription profiling by high throughput sequencing design - A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. - Person: Chris Stoeckert, Jie Zheng - MO_568 stimulus_or_stress_design - stimulus or stress design + A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + transcription profiling by high throughput sequencing design - + - + - + @@ -32639,7 +37245,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32653,61 +37259,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - G-CSF release|cytometric bead array - cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells - - - - - - - - - protein and DNA interaction identification objective + intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells - A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites. - Person: Chris Stoeckert, Jie Zheng - MO_933 binding_site_identification_design - protein and DNA interaction identification objective - - - - - - - - - - - - - - - - - - - epitope specific interleukin-22 production by T cells - - A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-22 production by T cells + A flow cytometry assay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells - + - + - + @@ -32716,7 +37285,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32730,42 +37299,24 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNF release|biological activity - assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - - - - - - - - - - - - - - - protocol optimization design + cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells - A study design where different protocols or protocol parameters are compared aims to find an optimized protocol - Person: Chris Stoeckert, Jie Zheng - MO_934 optimization_design - protocol optimization design + A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|bioassay + cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells - + - + - + @@ -32774,7 +37325,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -32788,113 +37339,20 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells. - IEDB - IEDB - IL-2 release|reporter gene assay - promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ChIP-chip design - - A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. - Person: Chris Stoeckert, Jie Zheng - ChIP-on-chip design - MO_933 binding_site_identification_design - ChIP-chip design - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - genetic characteristics information + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells - a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. - Person: Chris Stoeckert, Jie Zheng - MO_66 IndividualGeneticCharacteristics - MO definition: -The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. - -examples in ArrayExpress -wild_type -MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) -AlfpCre; SNF5 flox/knockout -p53 knock out -C57Bl/6 gp130lox/lox MLC2vCRE/+ -fer-15; fem-1 -df/df -pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - genetic characteristics information + A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells - + - + @@ -32907,7 +37365,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -32921,22 +37379,24 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|cytometric bead array - cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells + + A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|cytometric bead array + cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - + - + - + @@ -32945,7 +37405,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -32959,141 +37419,24 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|biological activity - assay measuring epitope specific interleukin-3 production by T cells - - - - - - - - - A T cell epitope dependent biological activity assay that detects T cell activation. - IEDB - IEDB - activation|biological activity - biological activity assay measuring epitope specific T cell activation - - - - - - - - - - - - - - - imprinting design - - A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. - Person: Chris Stoeckert, Jie Zheng - MO_914 imprinting_design - imprinting design - - - - - - - - - - - - - - - - - - - - - - - - - cell cycle design - - A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. - Person: Chris Stoeckert, Jie Zheng - MO_822 cell_cycle_design - cell cycle design - - - - - - - - - - - - - - - translation profiling design - - A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - translation profiling design - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cell type comparison design + ELISA measuring epitope specific interleukin-23 production by T cells - A study design that compares cells of different type, for example different cell lines. - Person: Chris Stoeckert, Jie Zheng - MO_764 cell_type_comparison_design - cell type comparison design + An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|ELISA + ELISA measuring epitope specific interleukin-23 production by T cells - + - + - + @@ -33102,7 +37445,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -33116,22 +37459,24 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - A cytometric bead array assay that detects RANTES production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|cytometric bead array - cytometric bead array assay measuring epitope specific RANTES production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release + + A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + perforin release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release - + - + - + @@ -33140,7 +37485,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -33154,60 +37499,117 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|bioassay - cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells + ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|ELISA + ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - + - - + + + - - + + + + + + + + + + + + + + + + + + + + genotyping by high throughput sequencing assay + + A genotyping assay that uses a high througput sequencer + James Malone + EFO:0002771 + genotyping by high throughput sequencing assay + + + + + + + + + + + + + - + - + - - + + + + + + + + + + + + + + + + + - A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|biological activity - assay measuring epitope specific interferon-gamma production by T cells + ChIP-chip assay + + An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin + Bjoern Petesr + James Malone + ChIP-on-chip assay + url:http://en.wikipedia.org/wiki/ChIP-on-chip + ChIP-chip assay - + - + - + @@ -33215,20 +37617,38 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - epitope specific interleukin-9 production by T cells + epitope specific T cell tolerance induction - A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-9 production by T cells + A process of T cell tolerance induction resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific T cell tolerance induction - + - + + + obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation + + An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + + + T cell degranulation by intracellular staining + obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation + true + + + + + + + @@ -33241,7 +37661,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -33255,37 +37675,25 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|biological activity - assay measuring epitope specific tumor necrosis factor production by T cells - - - - - - - - - ChIP-chip by tiling array design + assay measuring epitope specific interleukin-13 production by T cells - A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. - Person: Chris Stoeckert, Jie Zheng - Group: ArrayExpress production team - ChIP-chip by tiling array design + A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|biological activity + assay measuring epitope specific interleukin-13 production by T cells - + - - + + - + @@ -33297,125 +37705,70 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - dose response design + array platform variation design - A study design that examines the relationship between the size of the administered dose and the extent of the response. - Person: Chris Stoeckert, Jie Zheng - MO_485 dose_response_design - dose response design + A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. + Person: Chris Stoeckert, Jie Zheng + MO_899 array_platform_variation_design + array platform variation design - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin - ArrayExpress production team - EFO:0002762 - ChIP-chip by tiling array assay - - - - - - - - - - - - - - - - epitope specific helper T cell enhancement of T cell mediated immune response - - A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific helper T cell enhancement of T cell mediated immune response + assay measuring interleukin-9 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-9 release|biological activity + assay measuring interleukin-9 production by T cells - + - + - + @@ -33423,60 +37776,24 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - epitope specific interferon-beta production by T cells + epitope specific interleukin-3 production by T cells - A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interferon-beta production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - organism part comparison design - - A study design that compares tissues, regions, organs within or between organisms - Person: Chris Stoeckert, Jie Zheng - MO_953 organism_part_comparison_design - organism part comparison design + A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-3 production by T cells - + - + - + @@ -33485,7 +37802,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -33499,162 +37816,120 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - A flow cytometry assay that detects epitope specific granzyme B release by T cells - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - granzyme B release|intracellular staining - intracellular material detection measuring epitope specific granzyme B release by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells - + - + - - - - + + + + + + + + + - - protein binding site identification design - - A study design that investigates protein binding sites on nucleic acids. - Person: Chris Stoeckert, Jie Zheng - MO_933 binding_site_identification_design - protein binding site identification design + epitope specific lymphotoxin A production by T cells + + A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific lymphotoxin A production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - sex comparison design - - A study design that assays differences associated with an organism's sex, gender or mating type. - Person: Chris Stoeckert, Jie Zheng - MO_575 sex_design - sex comparison design + + + + + + + + + + + + + epitope specific interleukin-1 alpha production by T cells + + A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-1 alpha production by T cells - + - + - + - transcription profiling by tiling array design - - A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. - Person: Chris Stoeckert, Jie Zheng - MO_507 tiling_path_design - transcription profiling by tiling array design - - - - - - - - - - - - - - - - - - - + - cell differentiation design - - A study design that assays events associated with cell development or differentiation. - Person: Chris Stoeckert, Jie Zheng - MO_892 development_or_differentiation_design - cell differentiation design - - - - - - - - - transcription profiling design + ChIP-seq design - A study design that identifies forms and abundance of transcripts in the genome. - Person: Chris Stoeckert, Jie Zheng - MO_533 transcript_identification_design - transcription profiling design + A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. + Person: Chris Stoeckert, Jie Zheng + http://en.wikipedia.org/wiki/Chip-Sequencing + ChIP-seq design - + - + - + - operon identification design + translational bias design - A study design that identifies locations and members of operons in a genome. - Person: Chris Stoeckert, Jie Zheng - MO_772 operon_identification_design - operon identification design + A study design that characterizes the association of transcripts and translation machinery. + Person: Chris Stoeckert, Jie Zheng + MO_939 translational_bias_design + translational bias design - + - + - + @@ -33663,7 +37938,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -33677,42 +37952,24 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - A radio immuno assay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|radio immuno assay (RIA) - radio immuno assay measuring epitope specific interferon-gamma production by T cells - - - - - - - - - - - - - - - DNA methylation profiling by high throughput sequencing design + ELISA measuring epitope specific interleukin-3 production by T cells - A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. - Person: Chris Stoeckert, Jie Zheng - GROUP: ArrayExpress production team - DNA methylation profiling by high throughput sequencing design + An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|ELISA + ELISA measuring epitope specific interleukin-3 production by T cells - + - + - + @@ -33721,7 +37978,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -33735,60 +37992,49 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - granzyme B release|biological activity - assay measuring epitope specific granzyme B release by T cells + ELISA measuring epitope specific interleukin-1 alpha production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|ELISA + ELISA measuring epitope specific interleukin-1 alpha production by T cells - + - + - + - - - - - - - - - - - - - - - - - + + - A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|ICS - intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + epitope specific interleukin-27 production by T cells + + A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-27 production by T cells - + - + - + @@ -33797,7 +38043,7 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - + @@ -33808,120 +38054,47 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|ELISA - ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - - A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - - - - - - - - - all pairs design - - A study design in which all specimens are compared to every other specimen. - Person: Chris Stoeckert, Jie Zheng - MO_565 all_pairs - all pairs design - - - - - - - - - - - - - - - - A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology. - Person: Chris Stoeckert, Jie Zheng, Dan Berrios - Group: ArrayExpress production team - https://github.com/obi-ontology/obi/issues/854 - proteomic profiling by array design - - - - - - - - - q-value - PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. -"After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)" - - A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. -To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level. - PERS:Philippe Rocca-Serra - FDR adjusted p-value - Adapted from several sources, including -http://.en/wikipedia.org/wiki/False_discovery_rate -http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - q-value - - - - - - - - - - - - - - - genotyping design + in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response - A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. - Person: Chris Stoeckert, Jie Zheng - MO_560 genotyping_design - genotyping design + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + T cell help|in vivo assay + in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response - + - + @@ -33934,7 +38107,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -33948,47 +38121,79 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|biological activity - assay measuring epitope specific interleukin-2 production by T cells + assay measuring epitope specific transforming growth factor-beta production by T cells + + A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|biological activity + assay measuring epitope specific transforming growth factor-beta production by T cells - + - - + + + FWER adjusted p-value + http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html + + A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests + PERS:Philippe Rocca-Serra + adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) + FWER adjusted p-value + + + + + + + + + - - - + + + + + + + + + + + + + + + + - - epitope specific interleukin-15 production by T cells - - A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-15 production by T cells + + DNA methylation profiling by high throughput sequencing assay + + A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology + ArrayExpress production team + Helen Parkinson + James Malone + EFO:0002761 + DNA methylation profiling by high throughput sequencing assay - + - + - + @@ -33996,60 +38201,24 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - epitope specific macrophage inflammatory protein-1 gamma production by T cells + epitope specific transforming growth factor-beta production by T cells - A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific macrophage inflammatory protein-1 gamma production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - individual genetic characteristics comparison design - - A study design where genotype, haplotype, or other individual genetic characteristics are compared. - Person: Chris Stoeckert, Jie Zheng - MO_527 individual_genetic_characteristics_design - individual genetic characteristics comparison design + A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific transforming growth factor-beta production by T cells - + - + - + @@ -34058,7 +38227,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34072,18 +38241,20 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|biological activity - assay measuring epitope specific interleukin-1 beta production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells - + - + @@ -34096,7 +38267,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + + + + @@ -34110,22 +38284,24 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|biological activity - assay measuring epitope specific interleukin-4 production by T cells + assay measuring epitope specific cytotoxic T cell degranulation + + A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + degranulation|biological activity + assay measuring epitope specific cytotoxic T cell degranulation - + - + - + @@ -34134,7 +38310,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34148,22 +38324,50 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|biological activity - assay measuring epitope specific interleukin-6 production by T cells + cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells + + A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TGFb release|bioassay + cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells - + - - - - - + + + + + + + + + + + + + + RNA-seq assay + + An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. + James Malone + transcription profiling by high throughput sequencing + EFO:0002770 + RNA-seq assay + + + + + + + + + + + @@ -34172,7 +38376,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34186,22 +38390,24 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A reporter cell line analyte detection bioassay that detects tumor necrosis factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|bioassay - cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells + ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|ELISPOT + ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - + - + - + @@ -34210,7 +38416,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34224,42 +38430,87 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A flow cytometry assay that detects lymphotoxin A production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - lymphotoxin A/TNFb release|ICS - intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells + cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells + + A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|bioassay + cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + - pathogenicity design + genotyping by array assay - A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. - Person: Chris Stoeckert, Jie Zheng - MO_807 pathogenicity_design - pathogenicity design + A genotyping assay that uses an array + ArrayExpress production team + EFO:0002767 + genotyping by array assay - + - + - + + + + + + + + + epitope specific interleukin-16 production by T cells + + A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-16 production by T cells + + + + + + + + + + + @@ -34268,7 +38519,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34282,22 +38533,24 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - An enzyme-linked immunospot assay that detects interleukin-5 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-5 production by T cells + assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + + A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - + - + - + @@ -34306,7 +38559,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34320,22 +38573,44 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|biological activity - assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells - + - + + + + + + + + + DNA methylation profiling by array design + + A study design in which the methylation state of DNA is determined and is compared between samples using array technology. + Person: Chris Stoeckert, Jie Zheng + GROUP: ArrayExpress production team + DNA methylation profiling by array design + + + + + + + - + @@ -34344,7 +38619,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34358,18 +38633,20 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A cytometric bead array assay that detects interleukin-8 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-8 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-8 production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-22 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells - + - + @@ -34382,7 +38659,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34396,61 +38673,80 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|biological activity - assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + assay measuring epitope specific interleukin-16 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|biological activity + assay measuring epitope specific interleukin-16 production by T cells - + - - - - - - - - - - - - - - - + + + + + + + + - - + + + + + - - - + + + + + + ELISA measuring epitope specific IP-10 production by T cells + + An enzyme-linked immunosorbent assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|ELISA + ELISA measuring epitope specific IP-10 production by T cells + + + + + + + + + + + + - genetic modification design + translation profiling assay - A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. - Person: Chris Stoeckert, Jie Zheng - MO_447 genetic_modification_design - genetic modification design + An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. + James Malone + EFO:0001033 + translation profiling assay - + - + @@ -34463,7 +38759,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34477,122 +38773,138 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - granzyme B release|ELISA - ELISA measuring epitope specific granzyme B release by T cells + ELISA measuring epitope specific interleukin-15 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|ELISA + ELISA measuring epitope specific interleukin-15 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - epitope specific IP-10 production by T cells - - A process of IP-10 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific IP-10 production by T cells + cytometric bead array assay measuring epitope specific interleukin-12 production by T cells + + A cytometric bead array assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-12 production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + + in vitro design - A transcription profiling assay that uses array technology. - James Malone - RNA profiling by array assay - EFO:0002768 - https://sourceforge.net/p/obi/obi-terms/757/ - transcription profiling by array assay + A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. + Person: Chris Stoeckert, Jie Zheng + MO_347 in_vitro_design + in vitro design - + - + - + - - - - - - - + RNAi profiling by array design + + A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + RNAi profiling by array design + + + + + + + + + + + + + + - + + + + + + + + + + + - - - - - - strain comparison design + + + + + + ELISA measuring epitope specific lymphotoxin A production by T cells - A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. - Person: Chris Stoeckert, Jie Zheng - MO_462 strain_or_line_design - strain comparison design + An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + lymphotoxin A/TNFb release|ELISA + ELISA measuring epitope specific lymphotoxin A production by T cells - + - + - + @@ -34601,7 +38913,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34615,22 +38927,44 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|biological activity - assay measuring epitope specific monocyte chemotactic protein-1 production by T cells + cytometric bead array assay measuring epitope specific interleukin-5 production by T cells + + A cytometric bead array assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-5 production by T cells - + - + + + + + + + + + transcription profiling by array design + + A study design that identifies forms and abundance of transcripts in the genome using microarray technology. + Person: Chris Stoeckert, Jie Zheng + MO_533 transcript_identification_design + transcription profiling by array design + + + + + + + - + @@ -34639,7 +38973,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -34653,426 +38987,396 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A flow cytometry assay that detects interleukin-12 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells - + - + - + - + - - - - - - + + + + + + + + + + + + + + - An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. - IEDB - IEDB - disease exacerbation|in vivo assay - in vivo assay measuring T cell epitope specific disease exacerbation + assay measuring epitope specific interleukin-15 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|biological activity + assay measuring epitope specific interleukin-15 production by T cells - + - - + + - - - - - - - + - cell specimen - - A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. - Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ - PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl - MO_612 cell - cell specimen - - - - - - - - - - + + + + + - A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - ligand presentation|T cell recognition - monospecific T cell recognition assay measuring MHC ligand processing and presentation + disease state design + + A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. + Person: Chris Stoeckert, Jie Zheng + MO_902 disease_state_design + disease state design - + - + + + wild type organism genotype information + C57BL/6J wild type + + a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. + proposed and discussed on San Diego OBI workshop, March 2011 + Group: OBI group + Group: OBI group + wild type organism genotype information + + + + + + + - + - - + + + + + + + + + + + + + + + + + - epitope specific interleukin-17F production by T cells - - A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl - epitope specific interleukin-17F production by T cells - - - - - - - - - T cell epitope specific immune intervention - Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide + assay measuring epitope specific interleukin-17 production by T cells - An epitope specific immune intervention in which the induced response targets a T cell epitope - PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - T cell epitope specific immune intervention + A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|biological activity + assay measuring epitope specific interleukin-17 production by T cells - + - + - - - - - + + + + + - - + + + + + + + + + + + + - - - + + + - - specimen with known storage state - - A specimen for which it is known whether it has been subjected to storage of a specified type. - PERSON: Chris Stoeckert, Jie Zheng - MO_95 BiosourceType - specimen with known storage state + cytometric bead array assay measuring epitope specific interleukin-17 production by T cells + + A cytometric bead array assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-17 production by T cells - + - + - + - + - - - - - - + + + + + + + + + + + + + + - - - - - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. - IEDB - IEDB - tumor burden after challenge|in vivo assay - in vivo assay measuring T cell epitope specific protection from tumor challenge - - - - - - - - - lowess group transformation + cytometric bead array assay measuring epitope specific interleukin-10 production by T cells - A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. - Person: Elisabetta Manduchi - MO_861 lowess_group_normalization - lowess group transformation + A cytometric bead array assay that detects interleukin-10 production by T cells. + IEDB + IEDB + IL-10 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-10 production by T cells - + - + - - - - - - - - - - - - + - + - - - - - - - - - + + + + + + + + + + + + + + - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. - IEDB - IEDB - pathogen burden after challenge|in vivo assay - in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells - + - + - - - - - + - + - - - - - - + + + + + + + + + + + + + + - - - - - Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated. - A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. - IEDB - IEDB - phage display binding assay - - - - - - - - - - - - - - - lowess transformation + intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells - A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. - Person: Elisabetta Manduchi - MO_720 lowess_normalization - lowess transformation + A flow cytometry assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells - + - + - + - + - - - - - - + + + + + + + + + + + + + + - A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands - IEDB - IEDB - ligand presentation|mass spectrometry - mass spectrometry assay measuring MHC ligand processing and presentation + cytometric bead array assay measuring epitope specific interleukin-2 production by T cells + + A cytometric bead array assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-2 production by T cells - + - + + - - - - - + - - - - - - + + + + + + + + + + + + + + - - - A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). - PERSON: Chris Stoeckert, Jie Zheng - tissue specimen - MO_954 organism_part - specimen from organism - - - - - - - - - - - - - - - phage display library panning - Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind. - - Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection. - - Jason Greenbaum, Randi Vita, Bjoern Peters - IEDB, http://en.wikipedia.org/wiki/Phage_display - phage display library panning - - - - - - - - - lowess global transformation + cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells - A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. - Person: Elisabetta Manduchi - MO_692 lowess_global_normalization - lowess global transformation + A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|bioassay + cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells - + - + - + @@ -35081,7 +39385,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -35095,199 +39399,207 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A flow cytometry assay that detects transforming growth factor-beta production by T cells. - IEDB - IEDB - TGFb release|ICS - intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells + ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|ELISA + ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - + - - - - - - - - - - - - - - - + + + + + + + + - - + + + + + + + + + + + + - - - - - - - - - - - - cell collecting + + + + + + intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - A planned process that collects cells from culture. - PERSON: Chris Stoeckert, Jie Zheng - MO_982 harvest - cell collecting + A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|ICS + intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - + - - + + + - - + - - + + + + + + + + + - - A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. - IEDB - IEDB - in vivo activity|biological activity - biological activity assay measuring T cell epitope specific in vivo activity - - - - - - - - + - - + + + + + + + + + + + + - - + + - purified MHC molecule preparation - HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody - - A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. - BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general. - Bjoern Peters - purified MHC molecule preparation - - - - - - - - - - + + - disposition to be bound by an MHC protein complex - - Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. - PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters - MHC ligand disposition - IEDB - disposition to be bound by an MHC protein complex - - - - - - - - - B cell epitope specific immune intervention - Injecting a mouse with recombinant antibody targeting an anthrax epitope + RNAi profiling by array assay - An epitope specific immune intervention in which the induced response targets a B cell epitope - PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - B cell epitope specific immune intervention + An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. + James Malone + EFO:0001030 + RNAi profiling by array assay - + - - + + + + + + + + + + + + + + + + + genotype information + Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information - An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response - IEDB - tolerance induction - IEDB - epitope tolerance induction experiment + a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. + discussed on San Diego OBI workshop, March 2011 + Group: OBI group + Group: OBI group + genotype information - + - - + + - - + + + + + - A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. - IEDB - IEDB - ligand presentation|cellular MHC/mass spectrometry - mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC + RNA stability design + + A study design that examines the stability and/or decay of RNA transcripts. + Person: Chris Stoeckert, Jie Zheng + MO_553 RNA_stability_design + RNA stability design - + - + + + tiling microarray + + A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. + Person: Helen Parkinson + genome tiling array + EFO_0002704: tiling array + tiling microarray + + + + + + + - + @@ -35296,7 +39608,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -35310,239 +39622,188 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|cytometric bead array - cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + assay measuring epitope specific IP-10 production by T cells + + A T cell epitope specific cytokine production assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|biological activity + assay measuring epitope specific IP-10 production by T cells - + - + - + - + - - - - - - + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells - A binding assay that uses radioactivity detection as an indicator of binding. - Bjoern Peters - Randi Vita - IEDB - binding assay using radioactivity detection + A flow cytometry assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells - + - + + + + + + + + + + + + + + + + + + + + + + + + + species comparison design + + A study design that assays differences between distinct species. + Person: Chris Stoeckert, Jie Zheng + MO_675 species_design + species comparison design + + + + + + + - + - + + + + + - - - - - - + + + + + + + + + + + + + - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. - IEDB - IEDB - survival from challenge|in vivo assay - in vivo assay measuring T cell epitope specific protection based on survival + X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex + + A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|x-ray crystallography|angstroms + X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - A cell bound MHC binding assay that uses a T cell epitope recognition assay. - IEDB - IEDB - qualitative binding|cellular MHC/T cell inhibition - cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition - - - - - - - - - linear amplification - An example is the use of the T7 promoter for amplification by transcribing many RNA copies. + transcription profiling by RT-PCR design - An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. - PERSON: Chris Stoeckert, Jie Zheng - MO_997 linear_amplification - linear amplification - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. - IEDB - IEDB - helper response|biological activity - biological activity assay measuring epitope specific T cell helper activity + A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + transcription profiling by RT-PCR design - + - + - + - - - - - - - - - - - - - - - - - + + - A flow cytometry assay that detects interleukin-22 production by T cells. - IEDB - IEDB - IL-22 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells + epitope specific T cell enhancement of B cell mediated immune response + + A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific T cell enhancement of B cell mediated immune response - + - + - + @@ -35551,7 +39812,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -35565,420 +39826,365 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. - IEDB - IEDB - perforin release|biological activity - assay measuring epitope specific perforin release by T cells - - - - - - - - - atmosphere + ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. - PERSON: Chris Stoeckert, Jie Zheng - MO_219 atmosphere - atmosphere + An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|ELISA + ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - + - + - + - - - - - - - - - + + - - A binding assay that uses fluorescence detection as an indicator of binding. - Bjoern Peters - Randi Vita - IEDB - binding assay using fluorescence detection + epitope specific interleukin-21 production by T cells + + A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-21 production by T cells - + - - + + - - - - - - - - - + + - + - - - - - - - - - + + + + - A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - ligand presentation|coelution - coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand + flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex + + A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + T cell- APC binding|binding assay + flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex - + - - + + + - - + - + - - + + - - - - Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. - An assay in which a material's fluorescence is determined. - IEDB - IEDB - fluorescence detection assay - - - - - - - - - - - - - + + - epitope specific perforin production by T cells - - The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope. - Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation - PERSON: Bjoern Peters, Randi Vita - epitope specific perforin production by T cells - - - - - - - - - - + - - - - - - - - - - - + + + + + - MHC protein complex binding to ligand - The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex. - - The process in which a ligand binds to an MHC molecule to form a stable complex - 6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. - PERSON: Bjoern Peters; Randi Vita - IEDB - MHC protein complex binding to ligand - - - - - - - - - - + + + + + + + + + + + + - dissection - - A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. - PERSON: Chris Stoeckert, Jie Zheng - EFO_0003856 dissection - MO_374 dissect - dissection - - - - - - - - + - + - - - purification + + proteomic profiling by array assay - A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest - PERSON: Chris Stoeckert, Jie Zheng - MO_406 purify - purification + An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. + James Malone + EFO:0002765 + proteomic profiling by array assay - + - + - - - - - - + + + + + + - + - + - - - - - - - - - + + - - - - + + + + - - specimen with pre- or post-mortem status + cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells - A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. - organizational term, used in description of specimen that is created from known pre- or post-mortem status - PERSON: Chris Stoeckert, Jie Zheng - MO_84 OrganismStatus - specimen with pre- or post-mortem status + A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|bioassay + cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells - + - + - + - + - - - - - - + + + + + + + + + + + + + + - An efficacy of T cell epitope intervention experiment that detects a decrease in disease. - IEDB - IEDB - decreased disease|in vivo assay - in vivo assay measuring T cell epitope specific treatment of disease + ELISPOT assay measuring epitope specific granzyme B release by T cells + + An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + granzyme B release|ELISPOT + ELISPOT assay measuring epitope specific granzyme B release by T cells - + - - - sampling time measurement datum + + + + + + + + + microRNA profiling by array design - A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. - Person: Chris Stoeckert - time point - MO_738 timepoint - sampling time measurement datum + A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + microRNA profiling by array design - + - + - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - ligand presentation|Edman degradation - Edman degradation assay measuring MHC ligand processing and presentation - - - - - - - - - - - - - - - - - - - - - - A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. - IEDB - IEDB - ligand presentation|secreted MHC/mass spectrometry - mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC + in vivo assay measuring T cell epitope specific tolerance induction + + An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + tolerance|in vivo assay + in vivo assay measuring T cell epitope specific tolerance induction - + - - - - - - - - - disposition to be a product of antigen processing and presentation - The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER. + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells - A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. - IEDB - IEDB - disposition to be a product of antigen processing and presentation + A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells. + IEDB + IEDB + CCL5/RANTES release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells - + - + @@ -35991,7 +40197,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -36005,262 +40211,256 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A cytometric bead array assay that detects interleukin-17A production by T cells. - IEDB - IEDB - IL-17A release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-17A production by T cells + cytometric bead array assay measuring epitope specific interleukin-4 production by T cells + + A cytometric bead array assay that detects interleukin-4 production by T cells + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-4 production by T cells - + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific lymphotoxin A production by T cells + + A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + lymphotoxin A/TNFb release|biological activity + assay measuring epitope specific lymphotoxin A production by T cells + + + + + + + + - + - + - - + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|purified MHC/competitive/radioactivity - radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex + organism development design + + A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. + Person: Chris Stoeckert, Jie Zheng + MO_892 development_or_differentiation_design + organism development design - + - - - - - - - - + + - - + + - minimal inhibitory concentration + family history design - A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. - Created following request by Albert Goldfain - PERSON:Bjoern Peters - Bjoern Peters, coordinated with Albert Goldfain - minimal inhibitory concentration + A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. + Person: Chris Stoeckert, Jie Zheng + MO_544 family_history_design + family history design - + - + - + - - + + + + + + + + + + + + + + + + + - material maintenance service - model organism colony maintanance - - A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. - material maintenance service + ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + + An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + IEDB + IEDB + CXCL9/MIG release|ELISA + ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - + - - + + + transcription profiling identification objective + + A molecular feature identification objective that aims to characterize the abundance of transcripts + Person: Chris Stoeckert, Jie Zheng + Group: Penn Group + transcription profiling identification objective + + + + + + + + + - - + - + - - + + - - - - - - - - - - - - - - - - - - - - + + - - A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM - radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex + + DNA methylation profiling by array assay + + A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology + James Malone + EFO:0002759 + DNA methylation profiling by array assay - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM - radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex + assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|biological activity + assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - + - + - + @@ -36268,79 +40468,57 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + epitope specific granulocyte colony stimulating factor production by T cells - A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl - epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific granulocyte colony stimulating factor production by T cells - + - - + + + - - + - + - - + + - - - - - - - - - - - + + - - A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|lysate MHC/direct/fluorescence - fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex - - - - - - - - + + - - + - + - - + + @@ -36348,59 +40526,151 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - + + + + + + + + + + microRNA profiling by array assay + + An assay that analyses the microRNA component of the transcriptome using a microRNA array. + James Malone + EFO:0000753 + microRNA profiling by array assay + + + + + + + + + quality control testing design + + A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. + Person: Chris Stoeckert, Jie Zheng + MO_981 quality_control_testing_design + quality control testing design + + + + + + + + + + + + + + + - + - - + + + + + + clinical history design + + A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. + Person: Chris Stoeckert, Jie Zheng + MO_832 clinical_history_design + clinical history design + + + + + + + + + + + - - + + + + + + + + + + + + - A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM - fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells - + - + - + @@ -36409,7 +40679,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -36423,38 +40693,24 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells. - IEDB - IEDB - G-CSF release|ELISA - ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells - - - - - - - - - sequence assembly algorithm + cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Assembly Algorithm - NIAID GSCID-BRC - sequence assembly algorithm + A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|bioassay + cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - + - + - + @@ -36463,7 +40719,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -36477,248 +40733,200 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - A cytometric bead array assay that detects interleukin-17F production by T cells. - IEDB - IEDB - IL-17F release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-17F production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells + + A flow cytometry assay that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells - + - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand. - IEDB - IEDB - association constant KA|cellular MHC/direct/fluorescence|1/M - fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex - - - - - - - - - PDB file - The file found in the pdb with the identifier 3pe4 - -http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4 + detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. - PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum - PDB file + A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - epitope specific interleukin-17A production by T cells - - A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl - epitope specific interleukin-17A production by T cells - - - - - - - - - support service - An help desk for an instrument or a software. - - A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON; Carlo Torniai - support service + ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells + + An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|ELISA + ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells - + - + - + - + - - - - - - - - - - - - + + + + + + + + + + + + + + - material service - A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization - - A service which has a material entity as specified input and/or specified output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - material service - - - - - - - - - - - - - - - data analysis service - Statistaical analysis service, data visualization service - - A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - data analysis service + assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL4/MIP-1b release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - + - - - - - - - - - - - - - - - data service - Data analysis service such statistical abalysis or storage service such data backup. - - A service that has some information content entity as input and output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - Information content entity was used as specified input and output since it was more appropriate then data item or dataset. - data service + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-21 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|ELISA + ELISA measuring epitope specific interleukin-21 production by T cells - + - + - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + @@ -36726,26 +40934,43 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - + + + + + + + + + + + + + + + + + - A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. - IEDB - IEDB - half life|purified MHC/direct/fluorescence|min - fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex + in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity + + An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + type IV hypersensitivity (DTH)|in vivo skin test + in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity - + - + @@ -36758,7 +40983,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -36772,100 +40997,64 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A cytometric bead array assay that detects interleukin-9 production by T cells. - IEDB - IEDB - IL-9 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-9 production by T cells - - - - - - - - - data storage service - A service offering data backup - - A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - data storage service + cytometric bead array assay measuring epitope specific interleukin-13 production by T cells + + A cytometric bead array assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-13 production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + - - + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - + - - - - A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. - IEDB - IEDB - qualitative binding|purified MHC/competitive/fluorescence - fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells - + - + - + @@ -36873,274 +41062,170 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - epitope specific interleukin-7 production by T cells + epitope specific tumor necrosis factor superfamily cytokine production by T cells - A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl - epitope specific interleukin-7 production by T cells + A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific tumor necrosis factor superfamily cytokine production by T cells - + - - + + - - - - + + + + + + + + + + + + - equilibrium dissociation constant (KD) - KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb + allele information + genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information - A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) - PERSON: Bjoern Peters, Randi Vita - IEDB - equilibrium dissociation constant (KD) + a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. + discussed on San Diego OBI workshop, March 2011 + Person: Chris Stoeckert, Jie Zheng + MO_58 Allele + allele information - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|purified MHC/competitive/fluorescence|nM - fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex - - - - - - - - - - - - - - - training service - A service that offers training for a specific instrument or technique. A course to learn how to use a microscope - - A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - training service + cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells + + A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|cytometric bead array + cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. - IEDB - IEDB - dissociation constant KD|cellular MHC/competitive/fluorescence|nM - fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex - - - - - - - - - Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell. + ELISPOT assay measuring epitope specific interleukin-17 production by T cells - An assay that identifies an MHC ligand using a T cell response assay as a readout - PERSON: Randi Vita, Bjoern Peters - IEDB - - - T cell recognition - obsolete T cell recognition of eluted MHC ligand assay - true + An enzyme-linked immunospot assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-17 production by T cells - + - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex. - IEDB - IEDB - on rate|purified MHC/direct/fluorescence|nM^-1s^-1 - fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex + detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells - + - + @@ -37153,7 +41238,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -37167,86 +41252,150 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells. - IEDB - IEDB - IL-13 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - + - + + + + + + + + + + + + + + + + + + + + + + + + + post-transcriptional modification design + + A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. + post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases + Person: Chris Stoeckert, Jie Zheng + MO_392 cellular_modification_design + post-transcriptional modification design + + + + + + + - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-8 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-8 release|ELISA + ELISA measuring epitope specific interleukin-8 production by T cells + + + + + + + + + + + - - + + + + + + + + + + + + - A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. - IEDB - IEDB - dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM - fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 + cytometric bead array assay measuring epitope specific interleukin-6 production by T cells + + A cytometric bead array assay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-6 production by T cells - + - - + + + - - + - + - - + + @@ -37254,59 +41403,59 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + transcription profiling by RT-PCR assay + + A transcription profiling assay that uses reverse transcription PCR (RT-PCR). + Anna Farne + EFO:0002943 + transcription profiling by RT-PCR assay + + + + + + + + + + + - - - - - - - + + - A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|lysate MHC/competitive/radioactivity|nM - radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex + epitope specific chemokine (C-C motif) ligand 4 production by T cells + + A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific chemokine (C-C motif) ligand 4 production by T cells - + - + - + @@ -37315,7 +41464,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -37329,273 +41478,185 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells. - IEDB - IEDB - CCL3/MIP-1a release|ICS - intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + assay measuring epitope specific interleukin-23 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|biological activity + assay measuring epitope specific interleukin-23 production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + genetic alteration information + + a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. + proposed and discussed on San Diego OBI workshop, March 2011 + Group: OBI group + Group: OBI group + genetic alteration information + + + + + + + + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - + - comparative phenotypic assessment - - Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference - Philly workshop 2011 - Philly workshop 2011 - 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2 - comparative phenotypic assessment + cellular process design + + A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. + Person: Chris Stoeckert, Jie Zheng + MO_810 cellular_process_design + cellular process design - + - + - + - - + + - material analysis service - Services performing DNA sequencing or Cell Analysis - - A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - material analysis service - - - - - - - - - equilibrium association constant (KA) - KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. - - A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) - PERSON: Bjoern Peters, Randi Vita - IEDB - equilibrium association constant (KA) + epitope specific RANTES production by T cells + + A process of RANTES production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific RANTES production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|cellular MHC/competitive/radioactivity|nM - radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells - + - + - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + - A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cellular MHC - assay measuring binding of a cell-bound-MHC:ligand complex + cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|cytometric bead array + cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - + - - - access service - A service that provides acess to a mass spectrometer. - - A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service. - Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - access service + + + wild type allele information + + an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. + discussed on San Diego OBI workshop, March 2011 + Person: Chris Stoeckert, Jie Zheng + MO_605 genotype + wild type allele information - + - + @@ -37608,7 +41669,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -37622,367 +41683,407 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFSF11/RANKL release|ICS - intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + + A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL4/MIP-1b release|ICS + intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - + - + - + - - + + + + + + epitope specific granzyme B production by T cells + + A process of granzyme B production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific granzyme B production by T cells + + + + + + + + + + + - - - - - - - + + - A MHC:ligand binding assay that measures a binding constant. - IEDB - IEDB - binding constant|binding assay - assay measuring a binding constant of a MHC:ligand complex + epitope specific interleukin-8 production by T cells + + A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-8 production by T cells - + - - - rate measurement datum - The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. + + + + + + + + + injury design - A scalar measurement datum that represents the number of events occuring over a time interval - PERSON: Bjoern Peters, Randi Vita - IEDB - rate measurement datum + A study design in which the response of an organism(s) to injury or damage is studied. + Person: Chris Stoeckert, Jie Zheng + MO_726 injury_design + injury design - + - + - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + - A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|purified MHC - assay measuring binding of a purified-MHC:ligand complex + intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells + + A flow cytometry assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells - + - - - - - + + + + + + + + + + + + - + - + - - + + + + + + + + + - - - - + + + + organism status comparison design + + A study design that compares samples from live and dead organisms. + Person: Chris Stoeckert, Jie Zheng + MO_841 organism_status_design + organism status comparison design + + + + + + + + + + + - + + + + + + + + + + + - A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|lysate MHC/direct/radioactivity - radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex + ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + + An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL4/MIP-1b release|ELISA + ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - material storage service - A service that offers liquid nitrogen stroage. - - A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - material storage service + cytometric bead array assay measuring epitope specific interferon-gamma production by T cells + + A cytometric bead array assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|cytometric bead array + cytometric bead array assay measuring epitope specific interferon-gamma production by T cells - + - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. - IEDB - IEDB - half life|cellular MHC/direct/radioactivity|min - radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex + assay measuring epitope specific interleukin-18 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|biological activity + assay measuring epitope specific interleukin-18 production by T cells - + - + - - - - - - - - - - - - - - - + - - + + + + + + epitope specific interleukin-23 production by T cells + + A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-23 production by T cells + + + + + + + + + + + - - - - - - - - - - + + + + + + + + + + + - A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half life|cellular MHC/direct/fluorescence|min - fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex - - - - - - - - + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells - An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant. - PERSON: Bjoern Peters - IEDB - - obsolete cell lysate MHC binding constant determination assay - true + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells - + - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand. - IEDB - IEDB - half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM - fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex + detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells - + - + - + @@ -37991,7 +42092,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -38005,366 +42106,219 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A flow cytometry assay that detects interleukin-17F production by T cells. - IEDB - IEDB - IL-17F release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells - - - - - - - - - - - - - - - material processing service - A service for cell line creation. A service providing cel line immortalization. - - A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - material processing service + cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells + + A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|bioassay + cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. - IEDB - IEDB - dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM - radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|ICS + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - + + - A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half life|lysate MHC/direct/radioactivity|min - radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex + epitope specific monocyte chemotactic protein-1 production by T cells + + A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific monocyte chemotactic protein-1 production by T cells - + - - - - - - - - - 50% dissociation of binding temperature (Tm) - Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated. - + + + genotyping by array design - A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. - PERSON: Bjoern Peters, Randi Vita - melting temperature (Tm) - IEDB - 50% dissociation of binding temperature (Tm) + A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. + Person: Chris Stoeckert, Jie Zheng + MO_560 genotyping_design + genotyping by array design - + - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|lysate MHC/direct/radioactivity|1/s - radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex + assay measuring epitope specific interleukin-1 alpha production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|biological activity + assay measuring epitope specific interleukin-1 alpha production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells + + + + + + + + + + + - - + + + + + + + + + + + + - A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM - radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex + assay measuring epitope specific interferon-beta production by T cells + + A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|biological activity + assay measuring epitope specific interferon-beta production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand. - IEDB - IEDB - off rate|purified MHC/direct/fluorescence|1/s - fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex - - - - - - - + @@ -38377,7 +42331,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -38391,146 +42345,24 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells. - IEDB - IEDB - VEGF release|biological activity - assay measuring epitope specific vascular endothelial growth factor production by T cells - - - - - - - - - - - - - - - - - - - - - - - - equilibrium dissociation constant (KD) approximated by IC50 - - A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. - PERSON: Bjoern Peters, Randi Vita - http://dx.doi.org/10.1016/0006-2952(73)90196-2 - - equilibrium dissociation constant (KD) approximated by IC50 - - - - - - - - - - An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant. - PERSON: Bjoern Peters - IEDB - - obsolete cell bound MHC binding constant determination assay - true - - - - - - - - - - - - - - - DNA sequence data - The part of a FASTA file that contains the letters ACTGGGAA - - A sequence data item that is about the primary structure of DNA - OBI call; Bjoern Peters - OBI call; Melanie Courtout - 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. - DNA sequence data - - - - - - - - - - competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - - - cell lysate MHC competitive binding using radioactivity - obsolete cell lysate MHC competitive binding assay using radioactivity detection - true - - - - - - - - - - - - - - - - - - - - assigning gene property based on phenotypic assessment - - Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result. - Philly workshop 2011 - Philly workshop 2011 - assigning gene property based on phenotypic assessment - - - - - - - - + assay measuring epitope specific interleukin-12 production by T cells - An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. - PERSON: Bjoern Peters - IEDB - - obsolete purified MHC binding constant determination assay - true + A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|biological activity + assay measuring epitope specific interleukin-12 production by T cells - + - + - + @@ -38539,7 +42371,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -38550,40 +42382,26 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - A cytometric bead array assay that detects interleukin-22 production by T cells. - IEDB - IEDB - IL-22 release|cytometric bead array - cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + @@ -38591,201 +42409,222 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells. - IEDB - IEDB - VEGF release|ELISA - ELISA measuring epitope specific vascular endothelial growth factor production by T cells + in vivo assay measuring epitope specific T cell killing + + An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + cytotoxicity|in vivo assay + in vivo assay measuring epitope specific T cell killing - + - - + + + - - + - + - - + + - - + + + + + + + + - + - - - - + + + + + + + + + + + + + - - A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|lysate MHC - assay measuring binding of a cell-lysate-MHC:ligand complex - - - - - - - - - material transport service - A service for chemical disposal - - A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Carlo Torniai - material transport service - - - - - - - - - - - + + + + + - + - - + + - - - - equilibrium dissociation constant (KD) approximated by EC50 + + + + + + + + + + + + + + + + comparative genomic hybridization by array assay - A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. - PERSON: Bjoern Peters, Randi Vita - Assay Development: Fundamentals and Practices, By Ge Wu, page 74 - equilibrium dissociation constant (KD) approximated by EC50 - - - - - - - - - - direct binding assay measuring MHC ligand binding using MHC derived from a cell - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - - cell bound MHC direct binding - obsolete cell bound MHC direct binding assay - true + An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. + James Malone + array CGH + EFO:0000749 + comparative genomic hybridization by array assay - + - + - - - - - - - - - - + + + + + - half life of binding datum - The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. - - A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. - PERSON: Bjoern Peters, Randi Vita - IEDB - half life of binding datum + epitope specific cytotoxic T cell degranulation + + A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific cytotoxic T cell degranulation - + - + - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + - A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|purified MHC/direct/phage display - phage display binding assay measuring binding of a purified-MHC:ligand complex + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + stimulus or stress design + + A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. + Person: Chris Stoeckert, Jie Zheng + MO_568 stimulus_or_stress_design + stimulus or stress design + + + + + + + @@ -38798,7 +42637,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -38812,73 +42651,59 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A cytometric bead array assay that detects interleukin-7 production by T cells. - IEDB - IEDB - IL-7 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-7 production by T cells + cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells + + A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + G-CSF release|cytometric bead array + cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells - + - + + + protein and DNA interaction identification objective + + A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites. + Person: Chris Stoeckert, Jie Zheng + MO_933 binding_site_identification_design + protein and DNA interaction identification objective + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - + + - A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half life|purified MHC/direct/radioactivity|min - radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex + epitope specific interleukin-22 production by T cells + + A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-22 production by T cells - + - + @@ -38891,7 +42716,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -38905,38 +42730,44 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells. - IEDB - IEDB - IL-7 release|biological activity - assay measuring epitope specific interleukin-7 production by T cells + assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNF release|biological activity + assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - + - - - binding - A peptide binding to an MHC molecule to form a complex. + + + + + + + + + protocol optimization design - The process of material entities forming complexes. - 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. - PERSON: Bjoern Peters, Randi Vita - IEDB - binding + A study design where different protocols or protocol parameters are compared aims to find an optimized protocol + Person: Chris Stoeckert, Jie Zheng + MO_934 optimization_design + protocol optimization design - + - + - + @@ -38945,7 +42776,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -38959,459 +42790,421 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A flow cytometry assay that detects interleukin-17A production by T cells. - IEDB - IEDB - IL-17A release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells + promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells + + A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells. + IEDB + IEDB + IL-2 release|reporter gene assay + promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells - + - - + + - + + + + + + + - + - - - + + + + ChIP-chip design + + A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. + Person: Chris Stoeckert, Jie Zheng + ChIP-on-chip design + MO_933 binding_site_identification_design + ChIP-chip design + + + + + + + + - - - - - - - + - - - - + + + + + + + + + + + + + + + + + + + + + + + + - A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|purified MHC/direct/fluorescence - fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex + genetic characteristics information + + a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. + Person: Chris Stoeckert, Jie Zheng + MO_66 IndividualGeneticCharacteristics + MO definition: +The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. + +examples in ArrayExpress +wild_type +MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) +AlfpCre; SNF5 flox/knockout +p53 knock out +C57Bl/6 gp130lox/lox MLC2vCRE/+ +fer-15; fem-1 +df/df +pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) + + genetic characteristics information - + - - - Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody._ + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. - Bjoern Peters - Randi Vita - IEDB - direct binding assay + A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|cytometric bead array + cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - + - + - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + + + + + assay measuring epitope specific interleukin-3 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|biological activity + assay measuring epitope specific interleukin-3 production by T cells + + + + + + + + + + + - - + + + + + + + + + + + + - A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand. - IEDB - IEDB - half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM - fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex + assay measuring epitope specific T cell activation + + A T cell epitope dependent biological activity assay that detects T cell activation. + IEDB + IEDB + activation|biological activity + assay measuring epitope specific T cell activation - + - - + + - - - - - - - - - - - - + + - Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide._ - A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. - IEDB - IEDB - competitive inhibition of binding assay + imprinting design + + A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. + Person: Chris Stoeckert, Jie Zheng + MO_914 imprinting_design + imprinting design - + - - + + - + - + - - + + + cell cycle design + + A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. + Person: Chris Stoeckert, Jie Zheng + MO_822 cell_cycle_design + cell cycle design + + + + + + + + - - - - - - - - - - - - + + + translation profiling design + + A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + translation profiling design + + + + + + + + - - + + - + - - - - + + + + + + + + + - A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cellular MHC/competitive/fluorescence - fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex + cell type comparison design + + A study design that compares cells of different type, for example different cell lines. + Person: Chris Stoeckert, Jie Zheng + MO_764 cell_type_comparison_design + cell type comparison design - + - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|x-ray crystallography|angstroms - X-ray crystallography assay determining the 3D structure of a MHC:ligand complex - - - - - - - - - - - - - - - PDB file chain - The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex + cytometric bead array assay measuring epitope specific RANTES production by T cells - A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities - PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum - IEDB - PDB file chain + A cytometric bead array assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|cytometric bead array + cytometric bead array assay measuring epitope specific RANTES production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding. - IEDB - IEDB - half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM - cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition - - - - - - - - - data maintenance service - A database management service, a web hosting service. - - A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance. - PERSON: Carlo Torniai - PERSON: Matthew Brush - PERSON: Matthew Brush - data maintenance service - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. - IEDB - IEDB - qualitative binding|cellular MHC/competitive/radioactivity - radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex + cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells + + A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|bioassay + cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells - + - + @@ -39424,7 +43217,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -39438,22 +43231,49 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells. - IEDB - IEDB - G-CSF release|biological activity - assay measuring epitope specific granulocyte colony stimulating factor production by T cells + assay measuring epitope specific interferon-gamma production by T cells + + A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|biological activity + assay measuring epitope specific interferon-gamma production by T cells - + - + - + + + + + + + + + epitope specific interleukin-9 production by T cells + + A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-9 production by T cells + + + + + + + + + + + @@ -39462,7 +43282,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -39476,29 +43296,58 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A cytometric bead array assay that detects interleukin-21 production by T cells. - IEDB - IEDB - IL-21 release|cytometric bead array - cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells + assay measuring epitope specific tumor necrosis factor alpha production by T cells + + An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|biological activity + assay measuring epitope specific tumor necrosis factor alpha production by T cells - + - - + + + ChIP-chip by tiling array design + + A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. + Person: Chris Stoeckert, Jie Zheng + Group: ArrayExpress production team + ChIP-chip by tiling array design + + + + + + + + - - + + + + + + + + - + - - + + + + + + + + + @@ -39507,196 +43356,171 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - + - - - - - - - - A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cellular MHC/direct/radioactivity - radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex - - - - - - - - - - - - + - + + + + + + + + + + + - - + + - binding off rate measurement datum (koff) + dose response design - A rate measurement datum of how quickly bound complexes disassociate - PERSON: Bjoern Peters, Randi Vita - IEDB - binding off rate measurement datum (koff) + A study design that examines the relationship between the size of the administered dose and the extent of the response. + Person: Chris Stoeckert, Jie Zheng + MO_485 dose_response_design + dose response design - + - - + + + - - + - + - - + + - - - - - - - - - - - + + + + + + ChIP-chip by tiling array assay + + A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin + ArrayExpress production team + EFO:0002762 + ChIP-chip by tiling array assay + + + + + + + + + + + - - - - - - - + + - A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 50% dissociation temperature|purified MHC/direct/fluorescence|°C - fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex + epitope specific helper T cell enhancement of T cell mediated immune response + + A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific helper T cell enhancement of T cell mediated immune response - + - - + + - - - - - - - - - - + + + + + - - binding on rate measurement datum (kon) - - A rate measurement datum of how quickly bound complexes form - PERSON: Bjoern Peters, Randi Vita - IEDB - binding on rate measurement datum (kon) + + epitope specific interferon-beta production by T cells + + A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interferon-beta production by T cells - + - - + + - + + + + + + + - + - - + + - - - - - - - - - - - - - - - - - - A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cellular MHC/direct/fluorescence - fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex + organism part comparison design + + A study design that compares tissues, regions, organs within or between organisms + Person: Chris Stoeckert, Jie Zheng + MO_953 organism_part_comparison_design + organism part comparison design - + - + - + @@ -39705,7 +43529,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -39719,68 +43543,164 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. - IEDB - IEDB - TNFSF11/RANKL release|biological activity - assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + intracellular material detection measuring epitope specific granzyme B release by T cells + + A flow cytometry assay that detects epitope specific granzyme B release by T cells + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + granzyme B release|intracellular staining + intracellular material detection measuring epitope specific granzyme B release by T cells - + - - + + + + + + + + + protein binding site identification design + + A study design that investigates protein binding sites on nucleic acids. + Person: Chris Stoeckert, Jie Zheng + MO_933 binding_site_identification_design + protein binding site identification design + + + + + + + + - + + + + + + + - + - - + + + sex comparison design + + A study design that assays differences associated with an organism's sex, gender or mating type. + Person: Chris Stoeckert, Jie Zheng + MO_575 sex_design + sex comparison design + + + + + + + + - - + + + transcription profiling by tiling array design + + A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. + Person: Chris Stoeckert, Jie Zheng + MO_507 tiling_path_design + transcription profiling by tiling array design + + + + + + + + - + - - - - + + + + + + + + + - A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand. - IEDB - IEDB - qualitative binding|purified MHC/direct/radioactivity - radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex + cell differentiation design + + A study design that assays events associated with cell development or differentiation. + Person: Chris Stoeckert, Jie Zheng + MO_892 development_or_differentiation_design + cell differentiation design - + - + + + transcription profiling design + + A study design that identifies forms and abundance of transcripts in the genome. + Person: Chris Stoeckert, Jie Zheng + MO_533 transcript_identification_design + transcription profiling design + + + + + + + + + + + + + + + operon identification design + + A study design that identifies locations and members of operons in a genome. + Person: Chris Stoeckert, Jie Zheng + MO_772 operon_identification_design + operon identification design + + + + + + + - + @@ -39789,7 +43709,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -39803,22 +43723,44 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A flow cytometry assay that detects interleukin-8 production by T cells. - IEDB - IEDB - IL-8 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells + radio immuno assay measuring epitope specific interferon-gamma production by T cells + + A radio immuno assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|radio immuno assay (RIA) + radio immuno assay measuring epitope specific interferon-gamma production by T cells - + - + + + + + + + + + DNA methylation profiling by high throughput sequencing design + + A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. + Person: Chris Stoeckert, Jie Zheng + GROUP: ArrayExpress production team + DNA methylation profiling by high throughput sequencing design + + + + + + + - + @@ -39827,7 +43769,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -39841,1490 +43783,1466 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - A cytometric bead array assay that detects interleukin-23 production by T cells. - IEDB - IEDB - IL-23 release|cytometric bead array - cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells - - - - - - - - - - direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - - purified MHC direct binding - obsolete purified MHC direct binding assay - true + assay measuring epitope specific granzyme B release by T cells + + A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + granzyme B release|biological activity + assay measuring epitope specific granzyme B release by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - epitope specific vascular endothelial growth factor production by T cells - - A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl - epitope specific vascular endothelial growth factor production by T cells + intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + + A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|ICS + intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + + + + + ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + + An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|ELISA + ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + + + + + + + + + + + - - - - - - - + + - A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM - fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex + epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + + A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - + - - - - - - - - - GenBank ID + + + all pairs design - A CRID symbol uniquely indentifies the submitted GeneBank sequence record. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - GenBank Record ID - NIAID GSCID-BRC - GenBank ID + A study design in which all specimens are compared to every other specimen. + Person: Chris Stoeckert, Jie Zheng + MO_565 all_pairs + all pairs design - + - - + + - - + + - investigation description + proteomic profiling by array design - A textual entity that describes an investigation. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - study description - project description - NIAID GSCID-BRC - investigation description + A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology. + Person: Chris Stoeckert, Jie Zheng, Dan Berrios + Group: ArrayExpress production team + https://github.com/obi-ontology/obi/issues/854 + proteomic profiling by array design - + - - + + + q-value + PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. +"After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)" + + A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. +To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level. + PERS:Philippe Rocca-Serra + FDR adjusted p-value + Adapted from several sources, including +http://.en/wikipedia.org/wiki/False_discovery_rate +http://svitsrv25.epfl.ch/R-doc/library/qvalue.html + q-value + + + + + + + + - - + + - specimen identifier - - A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. - Person: Chris Stoeckert, Jie Zheng - specimen ID - NIAID GSCID-BRC metadata working group - Specimen ID - NIAID GSCID-BRC - specimen identifier - - - - - - - - - - - - 1 - - - - PubMed ID - - A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. - Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/ - Person: Chris Stoeckert, Jie Zheng - PMID - PubMed Identifier - Website: http://en.wikipedia.org/wiki/Wikipedia:PMID - Publication Citation - NIAID GSCID-BRC - PubMed ID - - - - - - - - - average depth of sequence coverage + genotyping design - An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Depth of Coverage - Average - NIAID GSCID-BRC - average depth of sequence coverage + A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. + Person: Chris Stoeckert, Jie Zheng + MO_560 genotyping_design + genotyping design - + - - - - - - - - - + + + + + + + + - - + + + + + + + + + + + + - - - - - - specimen collection time measurement datum + + + + + + assay measuring epitope specific interleukin-2 production by T cells - A time measurement datum that is the measure of the time when the specimens are collected. - Person: Chris Stoeckert, Jie Zheng - collection date - NIAID GSCID-BRC metadata working group - Specimen Collection Date - NIAID GSCID-BRC - specimen collection time measurement datum + A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|biological activity + assay measuring epitope specific interleukin-2 production by T cells - + - - - latitude coordinate measurement datum - - A measurement datum that is the measure of the latitude coordinate of a site. - Person: Chris Stoeckert, Jie Zheng - latitude - NIAID GSCID-BRC metadata working group - Specimen Collection Location - Latitude - NIAID GSCID-BRC - latitude coordinate measurement datum + + + + + + + + + + + + + epitope specific interleukin-15 production by T cells + + A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-15 production by T cells - + - - - longitude coordinate measurement datum - - A measurement datum that is the measure of the longitude coordinate of a site. - Person: Chris Stoeckert, Jie Zheng - longitude - NIAID GSCID-BRC metadata working group - Specimen Collection Location - Longitude - NIAID GSCID-BRC - longitude coordinate measurement datum + + + + + + + + + + + + + epitope specific macrophage inflammatory protein-1 gamma production by T cells + + A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific macrophage inflammatory protein-1 gamma production by T cells - + - - + + - - + + - investigation title - - A textual entity that denotes an investigation. - Person:Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - study title - project title - NIAID GSCID-BRC - investigation title - - - - - - - - - organism identification objective - - A biological feature identification objective to identify the organism species in a specimen. - Person: Chris Stoeckert, Jie Zheng - Penn Group - organism identification objective - - - - - - - - - + - + - - + + - - - - - - - - - - - - - - - - - - - An assay that identifies the organism species in a specimen. - Chris Stoeckert - Jie Zheng - NIAID GSCID-BRC metadata working group - organism identification assay - - - - - - - - - sequence annotation algorithm - - An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Annotation Algorithm - NIAID GSCID-BRC - sequence annotation algorithm - - - - - - - - - Bioinformatics Resource Center - - An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them. - Person: Chris Stoeckert, Jie Zheng - BRC - Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers - NIAID GSCID-BRC - Bioinformatics Resource Center - - - - - - - - - - - - - - - country name - - A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Website: http://en.wikipedia.org/wiki/Country - Specimen Collection Location - Country - NIAID GSCID-BRC - country name - - - - - - - - - - - - - - - investigation identifier - - A CRID symbol used to identify an investigation. - Person: Chris Stoeckert, Jie Zhneg - NIAID GSCID-BRC metadata working group - project ID - NIAID GSCID-BRC - investigation identifier - - - - - - - - - - - - - - - grant identifier + individual genetic characteristics comparison design - A CRID symbol used to identify a grant. - Person: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - grant ID - NIAID GSCID-BRC - grant identifier + A study design where genotype, haplotype, or other individual genetic characteristics are compared. + Person: Chris Stoeckert, Jie Zheng + MO_527 individual_genetic_characteristics_design + individual genetic characteristics comparison design - + - + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - + - + - - + + - - - - - - + + - Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column. - An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. - IEDB - IEDB - analytical chromatography + assay measuring epitope specific interleukin-1 beta production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|biological activity + assay measuring epitope specific interleukin-1 beta production by T cells - + - + - - - + + + + - + - + - - + + - - - - - - + + - Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure. - An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. - IEDB - IEDB - electron microscopy imaging assay + assay measuring epitope specific interleukin-4 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|biological activity + assay measuring epitope specific interleukin-4 production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye. - A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. - IEDB - IEDB - immuno staining assay + + assay measuring epitope specific interleukin-6 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|biological activity + assay measuring epitope specific interleukin-6 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - purified material - A mixture of peptide molecules that has been run through an HPLC column to remove 65 + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells - A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component - GROUP: OBI call - OBI conference call - purified material + A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|bioassay + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells - + - + - - - + + + + - + - + - - + + - - - - - - + + - A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell ._ - A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. - IEDB - IEDB - calorimetric binding assay + intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells + + A flow cytometry assay that detects lymphotoxin A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + lymphotoxin A/TNFb release|ICS + intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844). - A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). - IEDB - IEDB - antibody binding detection by fluorescence quenching - - - - - - - - - - - - + - grant + pathogenicity design - A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role. - Discussed on Feb 13, 2012 dev call. Details see the tracker: -https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 - Group: OBI - OBI - AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 - grant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|inhibition by antigen (~ IC50)|nM - antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 + A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. + Person: Chris Stoeckert, Jie Zheng + MO_807 pathogenicity_design + pathogenicity design - + - + - + - + + + + + + + + + + + - A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - histamine release|biological activity - biological activity assay measuring epitope specific Ig-mediated histamine release - - - - - - - - - - - - - - - - - - - - A B cell epitope dependent biological activity determination assay that detects antigen activation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - antigen activation|biological activity - biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation + ELISPOT assay measuring epitope specific interleukin-5 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-5 production by T cells - + - + - + - + + + + + + + + + + + - A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - complement-dependent cytotoxicity|biological activity - biological activity assay measuring epitope specific complement-dependent cytotoxicity + assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + + A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|biological activity + assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - + - + - + - + + + + + + + + + + + - A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - antibody-dependent cellular cytotoxicity|biological activity - biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity + cytometric bead array assay measuring epitope specific interleukin-8 production by T cells + + A cytometric bead array assay that detects interleukin-8 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-8 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-8 production by T cells - + - + - + - + + + + + + + + + + + - A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - neutralization |biological activity - biological activity assay measuring epitope specific immunoglobulin-mediated neutralization + assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|biological activity + assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - + - - - - - - - - + + + + + + + + + + + + + + + - + + + + + + + + - - - - - - A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - opsonization|biological activity - biological activity assay measuring epitope specific opsonization + + + + + + genetic modification design + + A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. + Person: Chris Stoeckert, Jie Zheng + MO_447 genetic_modification_design + genetic modification design - + - + - - - - - + - + + + + + + + + + + + - A calorimetric binding assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|calorimetry - calorimetry assay measuring binding of a B cell epitope:antibody complex + ELISA measuring epitope specific granzyme B release by T cells + + An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + granzyme B release|ELISA + ELISA measuring epitope specific granzyme B release by T cells - + - + - - - - - + - - - - - - - + + - An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|electron microscopy - electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex + epitope specific IP-10 production by T cells + + A process of IP-10 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific IP-10 production by T cells - + - - + + + - - - - - - + - - - - + + + + + + + + + + + + + - - A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|nuclear magnetic resonance (NMR) - NMR assay determining the 3D structure of a B cell epitope:antibody complex + + transcription profiling by array assay + + A transcription profiling assay that uses array technology. + James Malone + RNA profiling by array assay + EFO:0002768 + https://sourceforge.net/p/obi/obi-terms/757/ + transcription profiling by array assay - + - - - - - - - - - - - - + + + + + + + + + + + + + + + - + - - - - - - A cross-blocking assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|cross blocking - cross blocking assay measuring binding of a B cell epitope:antibody complex + + + + + + strain comparison design + + A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. + Person: Chris Stoeckert, Jie Zheng + MO_462 strain_or_line_design + strain comparison design - + - + - - - - - + - + + + + + + + + + + + - A radio immuno assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|radio immuno assay (RIA) - RIA measuring binding of a B cell epitope:antibody complex + assay measuring epitope specific monocyte chemotactic protein-1 production by T cells + + A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|biological activity + assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - + - + - - - - - + - + + + + + + + + + + + - An immunoblot assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|western blot - immunoblot assay measuring binding of a B cell epitope:antibody complex + intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells + + A flow cytometry assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells - + - + - - - - - + - + + + + + + + + + + + + + + + + - - - - A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|surface plasmon resonance (SPR) - plasmon resonance assay measuring binding of a B cell epitope:antibody complex - - - - - - - - - - - - - - - - + + + + + + - An immuno staining assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|immuno staining - immuno staining assay measuring binding of a B cell epitope:antibody complex + in vivo assay measuring T cell epitope specific disease exacerbation + + An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. + IEDB + IEDB + disease exacerbation|in vivo assay + in vivo assay measuring T cell epitope specific disease exacerbation - + - - - - - - - - - - - - - - - - - - - - - - An immunoprecipitation assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|immunoprecipitation - immunoprecipitation assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + + + + + + + cell specimen + + A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. + Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ + PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl + MO_612 cell + cell specimen - + - + + + + + + + + + + + + + + + + monospecific T cell recognition assay measuring MHC ligand processing and presentation + + A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + ligand presentation|T cell recognition + monospecific T cell recognition assay measuring MHC ligand processing and presentation + + + + + + + - + - - + + - - - + + + + epitope specific interleukin-17F production by T cells + + A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl + epitope specific interleukin-17F production by T cells + + + + + + + + + T cell epitope specific immune intervention + Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide + + An epitope specific immune intervention in which the induced response targets a T cell epitope + PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + T cell epitope specific immune intervention + + + + + + + + + + + + + + - - + + - - - + + + - A mass spectrometry assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|mass spectrometry - mass spectrometry assay measuring binding of a B cell epitope:antibody complex + + specimen with known storage state + + A specimen for which it is known whether it has been subjected to storage of a specified type. + PERSON: Chris Stoeckert, Jie Zheng + MO_95 BiosourceType + specimen with known storage state - + - + - + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + - + + + + + + - A phage display binding assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|phage display - phage display assay measuring binding of a B cell epitope:antibody complex + in vivo assay measuring T cell epitope specific protection after tumor burden challenge + + An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden. + IEDB + IEDB + tumor burden after challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection after tumor burden challenge - + - + + + lowess group transformation + + A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. + Person: Elisabetta Manduchi + MO_861 lowess_group_normalization + lowess group transformation + + + + + + + - + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + - + + + + + + - An electron microscopy imaging assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|electron microscopy - electron microscopy assay measuring binding of a B cell epitope:antibody complex + in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden + + An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden. + IEDB + IEDB + pathogen burden after challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden - + - + - + - - + + - + - - - - + + + + + + + + + + - An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|ELISA - ELISA measuring binding of a B cell epitope:antibody complex + phage display binding assay + Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated. + + A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. + IEDB + IEDB + phage display binding assay - + - + + + + + + + + + lowess transformation + + A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. + Person: Elisabetta Manduchi + MO_720 lowess_normalization + lowess transformation + + + + + + + - - - - - + - + - - - - + + + + + + - An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|ELISPOT - ELISPOT assay measuring binding of a B cell epitope:antibody complex + mass spectrometry assay measuring MHC ligand processing and presentation + + A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands + IEDB + IEDB + ligand presentation|mass spectrometry + mass spectrometry assay measuring MHC ligand processing and presentation - + - + - - - + + - + - - - - + + + + + + - A flow cytometry assay that detects the binding of an antigen with an antibody. - IEDB - IEDB - qualitative binding|flow cytometry - flow cytometry assay measuring binding of a B cell epitope:antibody complex + + specimen from organism + + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + PERSON: Chris Stoeckert, Jie Zheng + tissue specimen + MO_954 organism_part + specimen from organism - + - + + + + + + + + + phage display library panning + Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind. + + Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection. + + Jason Greenbaum, Randi Vita, Bjoern Peters + IEDB, http://en.wikipedia.org/wiki/Phage_display + phage display library panning + + + + + + + + + lowess global transformation + + A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. + Person: Elisabetta Manduchi + MO_692 lowess_global_normalization + lowess global transformation + + + + + + + @@ -41337,7 +45255,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -41351,97 +45269,233 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - A flow cytometry assay that detects epitope specific granzyme A release by T cells. - IEDB - IEDB - granzyme A release|intracellular staining - intracellular material detection assay measuring epitope specific granzyme A release by T cells + intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells + + A flow cytometry assay that detects transforming growth factor-beta production by T cells. + IEDB + IEDB + TGFb release|ICS + intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell collecting + + A planned process that collects cells from culture. + PERSON: Chris Stoeckert, Jie Zheng + MO_982 harvest + cell collecting + + + + + + + - + - + + + + + + + + + + + + + + + + + + + + + - + + + + + + - An analytical chromatography assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|chromatography - chromatography assay measuring binding of a B cell epitope:antibody complex + assay measuring T cell epitope specific in vivo activity + + A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. + IEDB + IEDB + in vivo activity|biological activity + assay measuring T cell epitope specific in vivo activity - + - - + + + - - - - - - - - - - - - - + - - - - - - - + + - - A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|nuclear magnetic resonance (NMR) - NMR assay measuring binding of a B cell epitope:antibody complex + + purified MHC molecule preparation + HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody + + A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. + BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general. + Bjoern Peters + purified MHC molecule preparation - + - + + + + + + + + + disposition to be bound by an MHC protein complex + + Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. + PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters + MHC ligand disposition + IEDB + disposition to be bound by an MHC protein complex + + + + + + + + + B cell epitope specific immune intervention + Injecting a mouse with recombinant antibody targeting an anthrax epitope + + An epitope specific immune intervention in which the induced response targets a B cell epitope + PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + B cell epitope specific immune intervention + + + + + + + + + epitope tolerance induction experiment + + An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response + IEDB + tolerance induction + IEDB + epitope tolerance induction experiment + + + + + + + + + + + + + + + + + + + + + + mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC + + A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. + IEDB + IEDB + ligand presentation|cellular MHC/mass spectrometry + mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC + + + + + + + - + @@ -41450,7 +45504,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -41464,208 +45518,96 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells. - IEDB - IEDB - granulysin release|ELISA - ELISA measuring epitope specific granulysin release by T cells + cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + + A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|cytometric bead array + cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells - + - + - + - + - - - - - - - - - - - - - - + + + + + + - A flow cytometry assay that detects epitope specific granulysin release by T cells. - IEDB - IEDB - granulysin release|intracellular staining - intracellular material detection assay measuring epitope specific granulysin release by T cells + binding assay using radioactivity detection + + A binding assay that uses radioactivity detection as an indicator of binding. + Bjoern Peters + Randi Vita + IEDB + binding assay using radioactivity detection - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - + + - - - - A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|cellular MHC/direct/fluorescence|1/s - fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex - - - - - - - - - - - - + - - - - - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - - A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|cellular MHC/direct/fluorescence|nM^-1s^-1 - fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - + + + + + + + + + + + + - - - - - - - - - - - - - - + @@ -41673,79 +45615,42 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - + + + + + + + - A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM - fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. PMID:17513562 - - A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. - Marcus Chibucos - Philippe Rocca-Serra - url:https://en.wikipedia.org/wiki/Two-hybrid_screening - split-ubiquitin assay + in vivo assay measuring T cell epitope specific protection based on survival + + An in vivo assay measuring T cell epitope specific protection from other challenge using survival. + IEDB + IEDB + survival from challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection based on survival - + - - + + - + @@ -41754,134 +45659,39 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - + + + + + + + + + - Studying protein-protein interactions via blot overlay or Far Western blot. PMID:15064457 - - An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. - Marcus Chibucos - Philippe Rocca-Serra - PMID:18079728 - far-western blot assay - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + - Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. PMID:11518275 - - An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. - Marcus Chibucos - Philippe Rocca-Serra - RNAse protection assay - RPA - PMID:16491611 - RNA protection assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. PMID:21918373 - - An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. - Marcus Chibucos - Philippe Rocca-Serra - EMSA - band shift assay - gel mobility shift assay - gel retardation assay - gel shift assay - PMID:6269071 - electrophoretic mobility shift assay - - - - - - - - - - - - - - - - - - + @@ -41890,155 +45700,108 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - + - - An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. - Marcus Chibucos - Philippe Rocca-Serra - PMID:17430206 - gene knock-down assay + cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition + + A cell bound MHC binding assay that uses a T cell epitope recognition assay. + IEDB + IEDB + qualitative binding|cellular MHC/T cell inhibition + cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846 - - A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). - Marcus Chibucos - Philippe Rocca-Serra - nano-CAGE - PMID:20543846 - nano-cap analysis of gene expression assay + + + linear amplification + An example is the use of the T7 promoter for amplification by transcribing many RNA copies. + + An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. + PERSON: Chris Stoeckert, Jie Zheng + MO_997 linear_amplification + linear amplification - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160 - - A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome - Marcus Chibucos - Philippe Rocca-Serra - CAGE - PMID:14663149 - cap analysis of gene expression assay + + in vivo assay measuring epitope specific T cell helper activity + + A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. + IEDB + IEDB + helper response|in vivo assay + in vivo assay measuring epitope specific T cell helper activity - + - + - + @@ -42047,7 +45810,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -42061,22 +45824,24 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells. - IEDB - IEDB - IL-17A release|ELISA - ELISA measuring epitope specific interleukin-17A production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells + + A flow cytometry assay that detects interleukin-22 production by T cells. + IEDB + IEDB + IL-22 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells - + - + - + @@ -42085,7 +45850,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + @@ -42099,372 +45864,541 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells. - IEDB - IEDB - IL-7 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells + assay measuring epitope specific perforin release by T cells + + A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. + IEDB + IEDB + perforin release|biological activity + assay measuring epitope specific perforin release by T cells - + - + + + atmosphere + + A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. + PERSON: Chris Stoeckert, Jie Zheng + MO_219 atmosphere + atmosphere + + + + + + + - + - - + + + + + + + + + - epitope specific granulysin production by T cells - - A process of granulysin production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific granulysin production by T cells + binding assay using fluorescence detection + + A binding assay that uses fluorescence detection as an indicator of binding. + Bjoern Peters + Randi Vita + IEDB + binding assay using fluorescence detection - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand + + A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + ligand presentation|coelution + coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand + + + + + + + - + - - + + + + + + + + + + + + - epitope specific granzyme A production by T cells - - A process of granzyme A production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific granzyme A production by T cells + fluorescence detection assay + Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. + + An assay in which a material's fluorescence is determined. + IEDB + IEDB + fluorescence detection assay - + - - - - - - - - - - - - - - + - - - + + + - - + + - - - - - - - - + + - Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. PMID:10627486 - - An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay. - Marcus Chibucos - Philippe Rocca-Serra - Y2H - url:https://en.wikipedia.org/wiki/Two-hybrid_screening - yeast 2-hybrid assay + epitope specific perforin production by T cells + + The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope. + Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation + PERSON: Bjoern Peters, Randi Vita + epitope specific perforin production by T cells - + - - - - - - - - - - - - - - + + - - - + + + - - + + + + + + + + + + + + + + + + + + + + + + - - + + + MHC protein complex binding to ligand + The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex. + + The process in which a ligand binds to an MHC molecule to form a stable complex + 6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. + PERSON: Bjoern Peters; Randi Vita + IEDB + MHC protein complex binding to ligand + + + + + + + + - + - The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. PMID:20300944 - - A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system. - Marcus Chibucos - Philippe Rocca-Serra - SRS - PMID:9154808 - Sos-recruitment assay + dissection + + A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. + PERSON: Chris Stoeckert, Jie Zheng + EFO_0003856 dissection + MO_374 dissect + dissection - + - - - - - - - - - - - - - - - + + - - - - - - - + + - - Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702 - - An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. - Marcus Chibucos - Philippe Rocca-Serra - Y1H - PMID:22218861 - yeast one-hybrid assay + + + purification + + A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest + PERSON: Chris Stoeckert, Jie Zheng + MO_406 purify + purification - + - - - - - - - - - - - - - - - + + - + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042 - - An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence - Marcus Chibucos - Philippe Rocca-Serra - B1H - url:http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system - bacterial one-hybrid assay + + + specimen with pre- or post-mortem status + + A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. + organizational term, used in description of specimen that is created from known pre- or post-mortem status + PERSON: Chris Stoeckert, Jie Zheng + MO_84 OrganismStatus + specimen with pre- or post-mortem status - + - - - + + + - + + + + + - - - + + + - + - - - - + + + + + + + + + - - + + - + - - - - - - + + + - - + + + + + + + + + + in vivo assay measuring T cell epitope specific treatment of disease + + An efficacy of T cell epitope intervention experiment that detects a decrease in disease. + IEDB + IEDB + decreased disease|in vivo assay + in vivo assay measuring T cell epitope specific treatment of disease + + + + + + + + + sampling time measurement datum + + A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. + Person: Chris Stoeckert + time point + MO_738 timepoint + sampling time measurement datum + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - + + Edman degradation assay measuring MHC ligand processing and presentation + + A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + ligand presentation|Edman degradation + Edman degradation assay measuring MHC ligand processing and presentation + + + + + + + + - + - - - - + + + + + + - - - - - - - Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449 - - An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity - Marcus Chibucos - Philippe Rocca-Serra - https://github.com/obi-ontology/obi/issues/788| - chromosome organization assay by fluorescence in-situ hybridization + mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC + + A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. + IEDB + IEDB + ligand presentation|secreted MHC/mass spectrometry + mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC - + - - + + - - + + - - - - + disposition to be a product of antigen processing and presentation + The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER. + + A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. + IEDB + IEDB + disposition to be a product of antigen processing and presentation + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - - - Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 - - An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. - Marcus Chibucos - Philippe Rocca-Serra - MSP - PMID:8790415 - methylation-specific polymerase chain reaction assay + + + + cytometric bead array assay measuring epitope specific interleukin-17A production by T cells + + A cytometric bead array assay that detects interleukin-17A production by T cells. + IEDB + IEDB + IL-17A release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-17A production by T cells - + - - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + - + @@ -42473,411 +46407,293 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - + - - - - - - - Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 - - An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. - Marcus Chibucos - Philippe Rocca-Serra - AIMS assay - intermethylated site amplification - PMID:18987810 - amplification of intermethylated sites assay + radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex + + A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|purified MHC/competitive/radioactivity + radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 - - An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. - Marcus Chibucos - Philippe Rocca-Serra - ISH - in situ hybridization - PMID:9021518 - in-situ hybridization assay - - - - - - - - - - + + - contact representative role - - A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. - Discussed on May 7, 2012 dev call -propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? -Whether it works for communicating author in manuscript or not? -Tracker: -https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178 - Person: Chris Stoeckert - NIAID GSCID-BRC - contact representative role + minimal inhibitory concentration + + A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. + Created following request by Albert Goldfain + PERSON:Bjoern Peters + Bjoern Peters, coordinated with Albert Goldfain + minimal inhibitory concentration - + - - - - - - - - - - - - - - - - - - + + + + + - - + + - - - - - - - - - - - An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). - Marcus Chibucos - Philippe Rocca-Serra - cytochalasin-induced inhibition of actin polymerization assay - - - - - - - - - molecular function identification objective - - is an objective specification which aims to discover molecular function realized by a molecular entity - PERSON:Philippe Rocca-Serra - OBI group - molecular function identification objective - - - - - - - - - cellular structure feature identification objective - - is an objective specification which aims to discover cellular structure properties - PERSON:Philippe Rocca-Serra - OBI group - cellular structure feature identification objective - - - - - - - - - - - - - - - - - - - - - - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - protection from fertility|in vivo assay - in vivo assay measuring B cell epitope specific protection from fertility + + + + material maintenance service + model organism colony maintanance + + A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. + material maintenance service - + - + - + - + - - + + + + + + + + + - + + + + + + + + + + - An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - tolerance|in vivo assay - in vivo assay measuring B cell epitope specific tolerance induction + radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex + + A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM + radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex - + - + - + - + - - + + + + + + + + + + + + + + + + + + + + + + + - + - - - - An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - hypersensitivity|in vivo assay - in vivo assay measuring B cell epitope specific induction of hypersensitivity - - - - - - - - - - - - - + + - A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - agglutination|biological activity - biological activity assay measuring epitope specific immune complex formation - - - - - - - - - - - - - - - - - - - - - - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - survival from challenge|in vivo assay - in vivo assay measuring B cell epitope specific protection based on survival + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex + + A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex - + - + - + - - - - - - - - - + + - An efficacy of B cell epitope intervention experiment that detects a decrease in disease. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - decreased disease|in vivo assay - in vivo assay measuring B cell epitope specific treatment of disease + epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + + A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl + epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - + - + - + - + - - + + + + + + + + + + + + + + + + + + - A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - in vivo activity|biological activity - biological activity assay measuring B cell epitope specific in vivo activity + fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex + + A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|lysate MHC/direct/fluorescence + fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex - + - - - + + + - + - + - - + + @@ -42888,353 +46704,382 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - - + + - - - - - - - - - - + + + + + + + - - + + - - - - - - Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. - A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. - IEDB - antibody inhibition of antibody binding - IEDB - antibody cross-blocking assay + + + + + + + + + + + + + + + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex - + - + - - - + + + + - + - + - - + + - - - - - - - - - + - Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. - An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. - IEDB - IEDB - immunoprecipitation assay + ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells + + An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells. + IEDB + IEDB + G-CSF release|ELISA + ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|inhibition by antigen - antigen inhibition assay measuring binding of a B cell epitope:antibody complex + + + sequence assembly algorithm + + An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. + Person: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Assembly Algorithm + NIAID GSCID-BRC + sequence assembly algorithm - + - - - - - - - - - + + + + + + + + - + - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - immunoglobulin binding to epitope - Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus + + + + + + cytometric bead array assay measuring epitope specific interleukin-17F production by T cells - a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). - PERSON: Bjoern Peters, Randi Vita - IEDB - immunoglobulin binding to epitope + A cytometric bead array assay that detects interleukin-17F production by T cells. + IEDB + IEDB + IL-17F release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-17F production by T cells - + - + - - - - - + - + - + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + - An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output. - IEDB - IEDB - qualitative binding|binding assay - assay measuring qualitative binding of a B cell epitope:antibody complex + fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand. + IEDB + IEDB + association constant KA|cellular MHC/direct/fluorescence|1/M + fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex - + - - - - - - + + + PDB file + The file found in the pdb with the identifier 3pe4 + +http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4 + + A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. + PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum + PDB file + + + + + + + + + + + - - - - - - - + + - - - - A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. - IEDB - IEDB - secondary in vitro activity|biological activity - biological activity assay measuring epitope specific activation of additional immune response in vitro + + + + epitope specific interleukin-17A production by T cells + + A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl + epitope specific interleukin-17A production by T cells - + - - - - - - - - - - - - - - - - - - - A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. - IEDB - IEDB - antibody activity inhibition|biological activity - biological activity assay measuring epitope specific antigen inhibition of antibody activity + + + support service + An help desk for an instrument or a software. + + A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON; Carlo Torniai + support service - + - + - + - + - - - + + - - + + - - + + + + + + - A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope. - IEDB - IEDB - biological activity|any method - assay measuring biological activity resulting from B cell epitope:antibody binding + material service + A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization + + A service which has a material entity as specified input and/or specified output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + material service - + - - - immunoglobulin mediated histamine release - - The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. - 4/26/12, BP: We want to import this from GO, which currently only has IgE mediated histamine release. We have requested the term, but need to use this as a placeholder in the meanwhile. - PERSON: Bjoern Peters, Randi Vita - IEDB - immunoglobulin mediated histamine release + + + + + + + + + data analysis service + Statistaical analysis service, data visualization service + + A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + data analysis service - + - + + + + + + + + + + + + + + + data service + Data analysis service such statistical abalysis or storage service such data backup. + + A service that has some information content entity as input and output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + Information content entity was used as specified input and output since it was more appropriate then data item or dataset. + data service + + + + + + + - + + + + + + + + + + + + + + + - + - + @@ -43243,263 +47088,235 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - A B cell epitope binding constant determination assay that measures the dissociation constant KD. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|binding assay|nM - assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex + + A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. + IEDB + IEDB + half life|purified MHC/direct/fluorescence|min + fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex - + - + - - - - - + - + + + + + + + + + + + - A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - binding constant|binding assay - assay measuring a binding constant of a B cell epitope:antibody complex - - - - - - - - - - - - - - - - - - - - - - - - - - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - protection from challenge|in vivo assay - in vivo assay measuring B cell epitope specific protection from challenge - - - - - - - - - - - - - - - - - - - - - - - - - - An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - disease exacerbation|in vivo assay - in vivo assay measuring B cell epitope specific disease exacerbation + cytometric bead array assay measuring epitope specific interleukin-9 production by T cells + + A cytometric bead array assay that detects interleukin-9 production by T cells. + IEDB + IEDB + IL-9 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-9 production by T cells - + - - - - A direct binding assay using a assay - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - - direct binding assay - obsolete B cell epitope direct binding assay - true + + + data storage service + A service offering data backup + + A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + data storage service - + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - B cell epitope specific opsonization - - opsonization resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific opsonization + + + + fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex + + A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + IEDB + IEDB + qualitative binding|purified MHC/competitive/fluorescence + fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex - + - + - + - + - B cell epitope specific immunoglobulin-mediated neutralization + epitope specific interleukin-7 production by T cells - immunoglobulin-mediated neutralization resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific immunoglobulin-mediated neutralization + A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl + epitope specific interleukin-7 production by T cells - + - - - - A competitive inhibition of binding assay using a assay - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - - competitive binding assay - obsolete B cell epitope competitive binding assay - true + + + + + + + + + equilibrium dissociation constant (KD) + KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb + + A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) + PERSON: Bjoern Peters, Randi Vita + IEDB + equilibrium dissociation constant (KD) - + - + - + - - + + + + + + + + + + + + - - - - B cell epitope specific complement-dependent cytotoxicity - - complement-dependent cytotoxicity resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific complement-dependent cytotoxicity - - - - - - - - - - - - - + + + + + + + + + + + + - - - - B cell epitope specific antibody-dependent cellular cytotoxicity - - antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific antibody-dependent cellular cytotoxicity - - - - - - - - - - - - + - + @@ -43508,39 +47325,91 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - A B cell epitope binding constant determination assay that measures the on rate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|binding assay|M^-1s^-1 - assay measuring the on rate [kon] of a B cell epitope:antibody complex + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex + + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|purified MHC/competitive/fluorescence|nM + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex - + - + + + + + + + + + training service + A service that offers training for a specific instrument or technique. A course to learn how to use a microscope + + A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + training service + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + @@ -43549,118 +47418,74 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - A B cell epitope binding constant determination assay that measures the association constant KA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|binding assay|1/nM - assay measuring the association constant [KA] of a B cell epitope:antibody complex + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + IEDB + IEDB + dissociation constant KD|cellular MHC/competitive/fluorescence|nM + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex - + - - - - - - - - - - B cell epitope specific immune complex formation - - immune complex formation resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific immune complex formation + + + obsolete T cell recognition of eluted MHC ligand assay + Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell. + + An assay that identifies an MHC ligand using a T cell response assay as a readout + PERSON: Randi Vita, Bjoern Peters + IEDB + + + T cell recognition + obsolete T cell recognition of eluted MHC ligand assay + true - + - + - + - - - - - + - - - - + + + + + + + + + - - - - A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|any method - 3D molecular structure determination assay of an antigen:antibody complex - - - - - - - - - - - - - - - - - - - B cell epitope specific hypersensitivity - - hypersensitivity resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific hypersensitivity - - - - - - - - - - - - + - + @@ -43669,128 +47494,95 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - A B cell epitope binding constant determination assay that measures the off rate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|binding assay|1/s - assay measuring the off rate [koff] of a B cell epitope:antibody complex + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex + + A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex. + IEDB + IEDB + on rate|purified MHC/direct/fluorescence|nM^-1s^-1 + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex - + - + - - - - - + - + + + + + + + + + + + - A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding| hemagglutination inhibition - viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex - - - - - - - - - - - - - - - - - - - B cell epitope specific histamine secretion mediated by immunoglobulin - - histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific histamine secretion mediated by immunoglobulin + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells. + IEDB + IEDB + IL-13 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells - + - + - - - - - + - + - - - - + + + + + + + + + - - - - A fluorescence quenching assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|quenching - quenching assay measuring binding of a B cell epitope:antibody complex - - - - - - - - - - - - + - + @@ -43806,22 +47598,52 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|radio immuno assay (RIA)|nM - RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 + + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. + IEDB + IEDB + dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -43831,7 +47653,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -43847,104 +47669,215 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|ELISA|nM - ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex + + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|lysate MHC/competitive/radioactivity|nM + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex - + - + - - - - - + - - - - - - - - - - + + + + + + + + + + + - A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|quenching|nM - quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells. + IEDB + IEDB + CCL3/MIP-1a release|ICS + intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - + - - - - - - - - - - - - + + + + + + + + + - + + + + + + + + + + + - - - - - + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + comparative phenotypic assessment + + Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference + Philly workshop 2011 + Philly workshop 2011 + 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2 + comparative phenotypic assessment + + + + + + + + + + + + + + - A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|surface plasmon resonance (SPR)|1/nM - surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex + material analysis service + Services performing DNA sequencing or Cell Analysis + + A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + material analysis service - + - + + + equilibrium association constant (KA) + KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. + + A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) + PERSON: Bjoern Peters, Randi Vita + IEDB + equilibrium association constant (KA) + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -43954,7 +47887,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -43970,254 +47903,324 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|surface plasmon resonance (SPR)|nM - surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex + + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|cellular MHC/competitive/radioactivity|nM + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex - + - + - + - - + + + + + + + + + + + + - - - - - - + - - + + - A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|quenching|1/nM - quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex + assay measuring binding of a cell-bound-MHC:ligand complex + + A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cellular MHC + assay measuring binding of a cell-bound-MHC:ligand complex - + - + + + access service + A service that provides acess to a mass spectrometer. + + A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service. + Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + access service + + + + + + + - - - - - + - - - - - - - - - - + + + + + + + + + + + - A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|calorimetry|1/nM - calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + + A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFSF11/RANKL release|ICS + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - + - + - + - + - - - - - - - - - - + - A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|calorimetry|nM - calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + assay measuring a binding constant of a MHC:ligand complex + + A MHC:ligand binding assay that measures a binding constant. + IEDB + IEDB + binding constant|binding assay + assay measuring a binding constant of a MHC:ligand complex - + - + + + rate measurement datum + The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. + + A scalar measurement datum that represents the number of events occuring over a time interval + PERSON: Bjoern Peters, Randi Vita + IEDB + rate measurement datum + + + + + + + - + - - + + + + + + + + + + + + - - - - - - + - - + + - An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|ELISA|1/nM - ELISA measuring the association constant [KA] of a B cell epitope:antibody complex + assay measuring binding of a purified-MHC:ligand complex + + A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|purified MHC + assay measuring binding of a purified-MHC:ligand complex - + - + - + - - + + + + + + + + + + + + - - - - - - + - - + + - A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|radio immuno assay (RIA)|1/nM - RIA measuring the association constant [KA] of a B cell epitope:antibody complex + radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex + + A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|lysate MHC/direct/radioactivity + radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex - + - - - - A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - - - X-ray crystallography [Ã…] - obsolete B cell epitope specific X-ray crystallography assay - true + + + + + + + + + + + + + material storage service + A service that offers liquid nitrogen stroage. + + A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + material storage service - + - + - + + + + + + + + + + + + + + + - + - + @@ -44226,39 +48229,55 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|x-ray crystallography|angstroms - X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex + radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex + + A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. + IEDB + IEDB + half life|cellular MHC/direct/radioactivity|min + radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex - + - + - + + + + + + + + + + + + + + + - + - + @@ -44267,39 +48286,71 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|surface plasmon resonance (SPR)|1/s - surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex + fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half life|cellular MHC/direct/fluorescence|min + fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex - + - + + + obsolete cell lysate MHC binding constant determination assay + + An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant. + PERSON: Bjoern Peters + IEDB + + obsolete cell lysate MHC binding constant determination assay + true + + + + + + + - + + + + + + + + + + + + + + + - + - + @@ -44308,80 +48359,131 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|quenching|1/s - quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand. + IEDB + IEDB + half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex - + - + - - - - - + - - - - - - - - - - + + + + + + + + + + + - A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|surface plasmon resonance (SPR)|M^-1s^-1 - surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex + intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells + + A flow cytometry assay that detects interleukin-17F production by T cells. + IEDB + IEDB + IL-17F release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells - + - + + + + + + + + + material processing service + A service for cell line creation. A service providing cel line immortalization. + + A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + material processing service + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + @@ -44390,181 +48492,296 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + - A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|quenching|M^-1s^-1 - quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 + + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. + IEDB + IEDB + dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells + radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex + + A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half life|lysate MHC/direct/radioactivity|min + radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex - + - + + + + + + + + + 50% dissociation of binding temperature (Tm) + Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated. + + + A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. + PERSON: Bjoern Peters, Randi Vita + melting temperature (Tm) + IEDB + 50% dissociation of binding temperature (Tm) + + + + + + + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + - A flow cytometry assay that detects interleukin-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells + radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex + + A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|lysate MHC/direct/radioactivity|1/s + radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + - An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex + + A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM + radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex + + A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand. + IEDB + IEDB + off rate|purified MHC/direct/fluorescence|1/s + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex - + - + - + @@ -44573,7 +48790,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -44587,98 +48804,151 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - A cytometric bead array assay that detects interleukin-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1a release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells + assay measuring epitope specific vascular endothelial growth factor production by T cells + + A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|biological activity + assay measuring epitope specific vascular endothelial growth factor production by T cells - + - + - - - - + + + + - - - - - - - - - - - + - - + + - An enzyme-linked immunospot assay that detects interferon-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|ELISPOT - ELISPOT assay measuring epitope specific interferon-beta production by T cells + equilibrium dissociation constant (KD) approximated by IC50 + + A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. + PERSON: Bjoern Peters, Randi Vita + http://dx.doi.org/10.1016/0006-2952(73)90196-2 + + equilibrium dissociation constant (KD) approximated by IC50 - + - - - - - + + + obsolete cell bound MHC binding constant determination assay + + An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant. + PERSON: Bjoern Peters + IEDB + + obsolete cell bound MHC binding constant determination assay + true + + + + + + + + + + + + + + + DNA sequence data + The part of a FASTA file that contains the letters ACTGGGAA + + A sequence data item that is about the primary structure of DNA + OBI call; Bjoern Peters + OBI call; Melanie Courtout + 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. + DNA sequence data + + + + + + + + + obsolete cell lysate MHC competitive binding assay using radioactivity detection + + competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + + + cell lysate MHC competitive binding using radioactivity + obsolete cell lysate MHC competitive binding assay using radioactivity detection + true + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + - - - - A flow cytometry assay that detects interferon-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|ICS - intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells + + + + assigning gene property based on phenotypic assessment + + Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result. + Philly workshop 2011 + Philly workshop 2011 + assigning gene property based on phenotypic assessment - + - + + + obsolete purified MHC binding constant determination assay + + An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. + PERSON: Bjoern Peters + IEDB + + obsolete purified MHC binding constant determination assay + true + + + + + + + - + @@ -44687,7 +48957,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -44701,18 +48971,20 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - G-CSF release|ICS - intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells + + A cytometric bead array assay that detects interleukin-22 production by T cells. + IEDB + IEDB + IL-22 release|cytometric bead array + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells - + - + @@ -44725,7 +48997,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -44739,227 +49011,212 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNb release|ELISA - ELISA measuring epitope specific interferon-beta production by T cells + ELISA measuring epitope specific vascular endothelial growth factor production by T cells + + An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|ELISA + ELISA measuring epitope specific vascular endothelial growth factor production by T cells - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + - A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - G-CSF release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells + assay measuring binding of a cell-lysate-MHC:ligand complex + + A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|lysate MHC + assay measuring binding of a cell-lysate-MHC:ligand complex - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - G-CSF release|ELISPOT - ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells + + + material transport service + A service for chemical disposal + + A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Carlo Torniai + material transport service - + - + - - - - + + + + - - - - - - - - - - - + - - + + - A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|cytometric bead array - cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + equilibrium dissociation constant (KD) approximated by EC50 + + A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. + PERSON: Bjoern Peters, Randi Vita + Assay Development: Fundamentals and Practices, By Ge Wu, page 74 + equilibrium dissociation constant (KD) approximated by EC50 - + - - - rats should be aged between 6 and 8 weeks and weight between 180-250grams + + + obsolete cell bound MHC direct binding assay - A directive information entity which defines and states a principle of standard by which selection process may take place. - Person: Philippe Rocca-Serra - selection rule - OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ - selection criterion + direct binding assay measuring MHC ligand binding using MHC derived from a cell + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + + cell bound MHC direct binding + obsolete cell bound MHC direct binding assay + true - + - + - - - - + + + + - - - - - - - - - - - + - - + + - An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|ELISPOT - ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + half life of binding datum + The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. + + A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. + PERSON: Bjoern Peters, Randi Vita + IEDB + half life of binding datum - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL9/MIG release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + phage display binding assay measuring binding of a purified-MHC:ligand complex + + A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|purified MHC/direct/phage display + phage display binding assay measuring binding of a purified-MHC:ligand complex - + - + - + @@ -44968,7 +49225,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -44982,98 +49239,81 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells. - IEDB - IEDB - CCL4/MIP-1b release|ELISPOT - ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + cytometric bead array assay measuring epitope specific interleukin-7 production by T cells + + A cytometric bead array assay that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-7 production by T cells - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + - - - - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL12/SDF-1 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - - - - - - - - - - - - - - - - - - - - - - - + + - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL13/BLC release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex + + A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half life|purified MHC/direct/radioactivity|min + radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex - + - + - + @@ -45082,7 +49322,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -45096,22 +49336,40 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL16 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells + assay measuring epitope specific interleukin-7 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|biological activity + assay measuring epitope specific interleukin-7 production by T cells - + - + + + binding + A peptide binding to an MHC molecule to form a complex. + + The process of material entities forming complexes. + 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. + PERSON: Bjoern Peters, Randi Vita + IEDB + binding + + + + + + + - + @@ -45120,7 +49378,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -45134,311 +49392,480 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL21/SLC release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells + + A flow cytometry assay that detects interleukin-17A production by T cells. + IEDB + IEDB + IL-17A release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells - + - - - - - - - - + + + + + + + + + - - - - - - - - - - - - + + - + + + + + + + + + + + + + + + + + + - - - - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL22/MDC release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + + + + fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex + + A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|purified MHC/direct/fluorescence + fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex - + - + + + direct binding assay + Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody._ + + A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. + Bjoern Peters + Randi Vita + IEDB + direct binding assay + + + + + + + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + - A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL4/MIP-1b release|cytometric bead array - cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex + + A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand. + IEDB + IEDB + half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM + fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex - + - - - - - - - - + + + + + + + + + - - - - - - - - - - - - + + - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells. - IEDB - IEDB - CCL4/MIP-1b release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + + + + + + competitive inhibition of binding assay + Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide._ + + A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. + IEDB + IEDB + competitive inhibition of binding assay - + - - - - - - - - + + + + + + + + + - - - - - - - - - - - - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells. - IEDB - IEDB - VEGF release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells + + + + fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cellular MHC/competitive/fluorescence + fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL19/MIP-3b release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells + X-ray crystallography assay determining the 3D structure of a MHC:ligand complex + + A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|x-ray crystallography|angstroms + X-ray crystallography assay determining the 3D structure of a MHC:ligand complex - + - + + + + + + + + + PDB file chain + The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex + + A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities + PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum + IEDB + PDB file chain + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + - A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|ICS - intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition + + A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding. + IEDB + IEDB + half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM + cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition - + - - + + + data maintenance service + A database management service, a web hosting service. + + A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance. + PERSON: Carlo Torniai + PERSON: Matthew Brush + PERSON: Matthew Brush + data maintenance service + + + + + + + + - + - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex - An Investigation agent role borne by a person or organization which -is realized in a specimen collection process. - Person: Jie Zheng, Chris Stoeckert - Penn Group - NIAID GSCID-BRC - specimen collector role + A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. + IEDB + IEDB + qualitative binding|cellular MHC/competitive/radioactivity + radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex - + - + - + @@ -45447,7 +49874,7 @@ is realized in a specimen collection process. - + @@ -45461,22 +49888,24 @@ is realized in a specimen collection process. - A flow cytometry assay that detects vascular endothelial growth factor production by T cells. - IEDB - IEDB - VEGF release|ICS - intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells + assay measuring epitope specific granulocyte colony stimulating factor production by T cells + + A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells. + IEDB + IEDB + G-CSF release|biological activity + assay measuring epitope specific granulocyte colony stimulating factor production by T cells - + - + - + @@ -45485,7 +49914,7 @@ is realized in a specimen collection process. - + @@ -45499,170 +49928,231 @@ is realized in a specimen collection process. - An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells. - IEDB - IEDB - VEGF release|ELISPOT - ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells + + A cytometric bead array assay that detects interleukin-21 production by T cells. + IEDB + IEDB + IL-21 release|cytometric bead array + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex + + A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cellular MHC/direct/radioactivity + radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex + + + + + + + + - - - - + + + + - - - - - - - - - - - + - - + + - - An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17F release|biological activity - assay measuring epitope specific interleukin-17F production by T cells + + binding off rate measurement datum (koff) + + A rate measurement datum of how quickly bound complexes disassociate + PERSON: Bjoern Peters, Randi Vita + IEDB + binding off rate measurement datum (koff) - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + + + + + + + + + + - An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17A release|biological activity - assay measuring epitope specific interleukin-17A production by T cells + fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex + + A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 50% dissociation temperature|purified MHC/direct/fluorescence|°C + fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex - + - - + + - - - - + + + + - - - - - - - - - - - + - - + + - - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL21/SLC release|biological activity - assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells + + binding on rate measurement datum (kon) + + A rate measurement datum of how quickly bound complexes form + PERSON: Bjoern Peters, Randi Vita + IEDB + binding on rate measurement datum (kon) - + - - - - - - - - + + + + + + + + + - - - - - - - - - - - - + + - + + + + + + + + + + + + + + + + + + - - - - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL19/MIP-3b release|biological activity - assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells + + + + fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cellular MHC/direct/fluorescence + fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex - + - + @@ -45675,7 +50165,7 @@ is realized in a specimen collection process. - + @@ -45689,60 +50179,72 @@ is realized in a specimen collection process. - A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells. - IEDB - IEDB - CXCL12/SDF-1 release|biological activity - assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells + assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells + + An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. + IEDB + IEDB + TNFSF11/RANKL release|biological activity + assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells - + - - - - - - - - + + + + + + + + + - - - - - - - - - - - - + + - + + + + + + + + + + + + + + + + + + - - - - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL22/MDC release|biological activity - assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + + + + radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex + + A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand. + IEDB + IEDB + qualitative binding|purified MHC/direct/radioactivity + radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex - + - + - + @@ -45751,7 +50253,7 @@ is realized in a specimen collection process. - + @@ -45765,22 +50267,24 @@ is realized in a specimen collection process. - A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL16 release|biological activity - assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells + + A flow cytometry assay that detects interleukin-8 production by T cells. + IEDB + IEDB + IL-8 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells - + - + - + @@ -45789,7 +50293,7 @@ is realized in a specimen collection process. - + @@ -45803,706 +50307,868 @@ is realized in a specimen collection process. - A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL13/BLC release|biological activity - assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells + + A cytometric bead array assay that detects interleukin-23 production by T cells. + IEDB + IEDB + IL-23 release|cytometric bead array + cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|ELISPOT - ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + + obsolete purified MHC direct binding assay + + direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + + purified MHC direct binding + obsolete purified MHC direct binding assay + true - + - + - + - - - - - - - - - - - - - - - - - + + - A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|cytometric bead array - cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + epitope specific vascular endothelial growth factor production by T cells + + A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl + epitope specific vascular endothelial growth factor production by T cells - + - + - + - + - - - - - - - - - - - - - - + + + + + + + + + - - - - A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - - - - - - - - - - - - + - - - - - - - - - - - - - - + + + + + + + + + - - - - A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|ICS - intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - - - - - - - - - - - + + + + - - - - - - - - - - - + - - - - An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL2/MCP-1 release|ELISPOT - ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - - - - - - - - - - - - - - - - - - - - - - - + + - A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|ICS - intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex + + A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM + fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL9/MIP-1g release|ELISPOT - ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + + + + + + + + + GenBank ID + + A CRID symbol uniquely indentifies the submitted GeneBank sequence record. + Person: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + GenBank Record ID + NIAID GSCID-BRC + GenBank ID - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects vascular endothelial growth factor production by T cells. - IEDB - IEDB - VEGF release|cytometric bead array - cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells + + + + + + + + + investigation description + + A textual entity that describes an investigation. + Person: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + study description + project description + NIAID GSCID-BRC + investigation description - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells. - IEDB - IEDB - TNF release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + + + + + + + + specimen identifier + + A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. + Person: Chris Stoeckert, Jie Zheng + specimen ID + NIAID GSCID-BRC metadata working group + Specimen ID + NIAID GSCID-BRC + specimen identifier - + - - - - - - - - - - - - - - - - - - - - - + + + + + + 1 + + + + PubMed ID + + A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. + Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/ + Person: Chris Stoeckert, Jie Zheng + PMID + PubMed Identifier + Website: http://en.wikipedia.org/wiki/Wikipedia:PMID + Publication Citation + NIAID GSCID-BRC + PubMed ID + + + + + + + + + average depth of sequence coverage + + An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. + Person: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Depth of Coverage - Average + NIAID GSCID-BRC + average depth of sequence coverage + + + + + + + + + + + + + + + + + + - - - - - - A flow cytometry assay that detects RANTES production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|ICS - intracellular cytokine staining assay measuring epitope specific RANTES production by T cells + + + + + + specimen collection time measurement datum + + A time measurement datum that is the measure of the time when the specimens are collected. + Person: Chris Stoeckert, Jie Zheng + collection date + NIAID GSCID-BRC metadata working group + Specimen Collection Date + NIAID GSCID-BRC + specimen collection time measurement datum - + - - - - - - - - + + + latitude coordinate measurement datum + + A measurement datum that is the measure of the latitude coordinate of a site. + Person: Chris Stoeckert, Jie Zheng + latitude + NIAID GSCID-BRC metadata working group + Specimen Collection Location - Latitude + NIAID GSCID-BRC + latitude coordinate measurement datum + + + + + + + + + longitude coordinate measurement datum + + A measurement datum that is the measure of the longitude coordinate of a site. + Person: Chris Stoeckert, Jie Zheng + longitude + NIAID GSCID-BRC metadata working group + Specimen Collection Location - Longitude + NIAID GSCID-BRC + longitude coordinate measurement datum + + + + + + + + + + + + + + + investigation title + + A textual entity that denotes an investigation. + Person:Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + study title + project title + NIAID GSCID-BRC + investigation title + + + + + + + + + organism identification objective + + A biological feature identification objective to identify the organism species in a specimen. + Person: Chris Stoeckert, Jie Zheng + Penn Group + organism identification objective + + + + + + + + + + + + + + + - - - - - - - - - - - - + + - + + + + + + + + + + + + - - - - An enzyme-linked immunospot assay that detects RANTES production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL5/RANTES release|ELISPOT - ELISPOT assay measuring epitope specific RANTES production by T cells + + + + + + + + + + organism identification assay + + An assay that identifies the organism species in a specimen. + Chris Stoeckert + Jie Zheng + NIAID GSCID-BRC metadata working group + organism identification assay - + - + + + sequence annotation algorithm + + An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. + Person: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Annotation Algorithm + NIAID GSCID-BRC + sequence annotation algorithm + + + + + + + + + Bioinformatics Resource Center + + An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them. + Person: Chris Stoeckert, Jie Zheng + BRC + Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers + NIAID GSCID-BRC + Bioinformatics Resource Center + + + + + + + + + + + + + + + country name + + A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. + Person: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Website: http://en.wikipedia.org/wiki/Country + Specimen Collection Location - Country + NIAID GSCID-BRC + country name + + + + + + + + + + + + + + + investigation identifier + + A CRID symbol used to identify an investigation. + Person: Chris Stoeckert, Jie Zhneg + NIAID GSCID-BRC metadata working group + project ID + NIAID GSCID-BRC + investigation identifier + + + + + + + + + + + + + + + grant identifier + + A CRID symbol used to identify a grant. + Person: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + grant ID + NIAID GSCID-BRC + grant identifier + + + + + + + - - - - + + + - + - + - - + + - - - - - - An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells. - IEDB - IEDB - lymphotoxin A/TNFb release|ELISPOT - ELISPOT assay measuring epitope specific lymphotoxin A production by T cells - - - - - - - - - - - - - - - + + + + + + + + + - + - - + + - - + + + + + + - A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL3/MIP-1a release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + analytical chromatography + Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column. + + An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. + IEDB + IEDB + analytical chromatography - + - + - - - - + + + - + - + - - + + - - + + + + + + - A cytometric bead array assay that detects lymphotoxin A production by T cells. - IEDB - IEDB - lymphotoxin A/TNFb release|cytometric bead array - cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells + electron microscopy imaging assay + Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure. + + An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. + IEDB + IEDB + electron microscopy imaging assay - + - - + + + - - + - - - - - - - - - - - - - - + + + + + + + + + + + + + - - A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells. - IEDB - IEDB - lymphotoxin A/TNFb release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells + + immuno staining assay + Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye. + + A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. + IEDB + IEDB + immuno staining assay - + - + - + - - - - - - - - - - - - - - - - - + + - An enzyme-linked immunospot assay that detects IP-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|ELISPOT - ELISPOT assay measuring epitope specific IP-10 production by T cells + purified material + A mixture of peptide molecules that has been run through an HPLC column to remove 65 + + A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component + GROUP: OBI call + OBI conference call + purified material - + - + - - - - + + + - + - + - - + + - - + + + + + + - A flow cytometry assay that detects IP-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CXCL10/IP-10 release|ICS - intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells + calorimetric binding assay + A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell ._ + + A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. + IEDB + IEDB + calorimetric binding assay - + - - - - - + + + + + - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - An enzyme-linked immunospot assay that detects interleukin-9 production by T cells. - IEDB - IEDB - IL-9 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-9 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + antibody binding detection by fluorescence quenching + The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844). + + A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). + IEDB + IEDB + antibody binding detection by fluorescence quenching - + - + + + + + + + + + grant + + A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role. + Discussed on Feb 13, 2012 dev call. Details see the tracker: +https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 + Group: OBI + OBI + AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 + grant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 + + A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|inhibition by antigen (~ IC50)|nM + antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 + + + + + + + - + @@ -46511,10 +51177,10 @@ is realized in a specimen collection process. - + - + @@ -46522,40 +51188,16 @@ is realized in a specimen collection process. - - - - A flow cytometry assay that detects interleukin-9 production by T cells. - IEDB - IEDB - IL-9 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells - - - - - - - - - - - - - - - - - - - - + + + + @@ -46563,22 +51205,60 @@ is realized in a specimen collection process. - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells. - IEDB - IEDB - IL-9 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells + assay measuring epitope specific Ig-mediated histamine release + + A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + histamine release|biological activity + assay measuring epitope specific Ig-mediated histamine release - + - + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific immunoglobulin-mediated antigen activation + + A B cell epitope dependent biological activity determination assay that detects antigen activation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + antigen activation|biological activity + assay measuring epitope specific immunoglobulin-mediated antigen activation + + + + + + + - + @@ -46587,10 +51267,10 @@ is realized in a specimen collection process. - + - + @@ -46598,25 +51278,41 @@ is realized in a specimen collection process. + + + + + + + + + + + + + + - An enzyme-linked immunospot assay that detects interleukin-8 production by T cells. - IEDB - IEDB - IL-8 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-8 production by T cells + assay measuring epitope specific complement-dependent cytotoxicity + + A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro . + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + complement-dependent cytotoxicity|biological activity + assay measuring epitope specific complement-dependent cytotoxicity - + - + - + @@ -46625,10 +51321,10 @@ is realized in a specimen collection process. - + - + @@ -46636,25 +51332,77 @@ is realized in a specimen collection process. + + + + + + + + + + + + + + - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells. - IEDB - IEDB - IL-8 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells + assay measuring epitope specific antibody-dependent cellular cytotoxicity + + A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + antibody-dependent cellular cytotoxicity|biological activity + assay measuring epitope specific antibody-dependent cellular cytotoxicity - + - + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific immunoglobulin-mediated neutralization + + A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + neutralization |biological activity + assay measuring epitope specific immunoglobulin-mediated neutralization + + + + + + + - + @@ -46663,10 +51411,10 @@ is realized in a specimen collection process. - + - + @@ -46674,691 +51422,551 @@ is realized in a specimen collection process. + + + + + + + + + + + + + + - An enzyme-linked immunospot assay that detects interleukin-3 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-3 production by T cells + assay measuring epitope specific opsonization + + A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro . + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + opsonization|biological activity + assay measuring epitope specific opsonization - + - + - + + + + + - - - - - - - - - - - + - An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-7 release|ELISA - ELISA measuring epitope specific interleukin-7 production by T cells + calorimetry assay measuring binding of a B cell epitope:antibody complex + + A calorimetric binding assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|calorimetry + calorimetry assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - An enzyme-linked immunospot assay that detects interleukin-7 production by T cells. - IEDB - IEDB - IL-7 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-7 production by T cells + electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex + + An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|electron microscopy + electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A flow cytometry assay that detects interleukin-7 production by T cells. - IEDB - IEDB - IL-7 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells + NMR assay determining the 3D structure of a B cell epitope:antibody complex + + A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|nuclear magnetic resonance (NMR) + NMR assay determining the 3D structure of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A flow cytometry assay that detects interleukin-27 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells + cross blocking assay measuring binding of a B cell epitope:antibody complex + + A cross-blocking assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|cross blocking + cross blocking assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A cytometric bead array assay that detects interleukin-3 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-3 production by T cells + RIA measuring binding of a B cell epitope:antibody complex + + A radio immuno assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|radio immuno assay (RIA) + RIA measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-3 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells + immunoblot assay measuring binding of a B cell epitope:antibody complex + + An immunoblot assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|western blot + immunoblot assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. - IEDB - IEDB - granzyme A release|biological activity - assay measuring epitope specific granzyme A release by T cells + plasmon resonance assay measuring binding of a B cell epitope:antibody complex + + A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|surface plasmon resonance (SPR) + plasmon resonance assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. - IEDB - IEDB - granulysin release|biological activity - assay measuring epitope specific granulysin release by T cells + immuno staining assay measuring binding of a B cell epitope:antibody complex + + An immuno staining assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|immuno staining + immuno staining assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A cytometric bead array assay that detects interleukin-27 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-27 production by T cells + immunoprecipitation assay measuring binding of a B cell epitope:antibody complex + + An immunoprecipitation assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|immunoprecipitation + immunoprecipitation assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A flow cytometry assay that detects interleukin-23 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells + mass spectrometry assay measuring binding of a B cell epitope:antibody complex + + A mass spectrometry assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|mass spectrometry + mass spectrometry assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - An enzyme-linked immunospot assay that detects interleukin-27 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-27 production by T cells + phage display assay measuring binding of a B cell epitope:antibody complex + + A phage display binding assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|phage display + phage display assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-27 release|ELISA - ELISA measuring epitope specific interleukin-27 production by T cells + electron microscopy assay measuring binding of a B cell epitope:antibody complex + + An electron microscopy imaging assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|electron microscopy + electron microscopy assay measuring binding of a B cell epitope:antibody complex - + - + - + + + + + - - - - - - - - - - - + - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells + ELISA measuring binding of a B cell epitope:antibody complex + + An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|ELISA + ELISA measuring binding of a B cell epitope:antibody complex - + - + - + - - + + - - - - - A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific chemokine (C-X-C motif) ligand 13 production by T cells - - - - - - - - - - - - - - - - - - - - - - + - An enzyme-linked immunospot assay that detects interleukin-18 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-18 production by T cells - - - - - - - - - - - - - - - - - - - - A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - - - - - - - - - - - - - - - - - - - - A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific chemokine (C-C motif) ligand 22 production by T cells + ELISPOT assay measuring binding of a B cell epitope:antibody complex + + An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|ELISPOT + ELISPOT assay measuring binding of a B cell epitope:antibody complex - + - + - + - - + + - - - - - A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - - - - - - - - - - - - - - - - - - - - - - + - An enzyme-linked immunospot assay that detects interleukin-22 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-22 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-22 production by T cells + flow cytometry assay measuring binding of a B cell epitope:antibody complex + + A flow cytometry assay that detects the binding of an antigen with an antibody. + IEDB + IEDB + qualitative binding|flow cytometry + flow cytometry assay measuring binding of a B cell epitope:antibody complex - + - + - + @@ -47367,7 +51975,7 @@ is realized in a specimen collection process. - + @@ -47381,146 +51989,103 @@ is realized in a specimen collection process. - An enzyme-linked immunospot assay that detects interleukin-23 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-23 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-23 production by T cells + intracellular material detection assay measuring epitope specific granzyme A release by T cells + + A flow cytometry assay that detects epitope specific granzyme A release by T cells. + IEDB + IEDB + granzyme A release|intracellular staining + intracellular material detection assay measuring epitope specific granzyme A release by T cells - + - + - + - - + + - - - - - A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific chemokine (C-C motif) ligand 21 production by T cells - - - - - - - - - - - - - - - - - - - - - - + - A flow cytometry assay that detects interleukin-18 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells + chromatography assay measuring binding of a B cell epitope:antibody complex + + An analytical chromatography assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|chromatography + chromatography assay measuring binding of a B cell epitope:antibody complex - + - + - + - - + + + + + + + + + + + + + - - - - - A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt - epitope specific chemokine (C-C motif) ligand 19 production by T cells - - - - - - - - - - - - - - - - - - - - - - + - An enzyme-linked immunospot assay that detects interleukin-21 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-21 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-21 production by T cells + NMR assay measuring binding of a B cell epitope:antibody complex + + A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|nuclear magnetic resonance (NMR) + NMR assay measuring binding of a B cell epitope:antibody complex - + - + - + @@ -47529,7 +52094,7 @@ is realized in a specimen collection process. - + @@ -47543,22 +52108,24 @@ is realized in a specimen collection process. - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + ELISA measuring epitope specific granulysin release by T cells + + An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells. + IEDB + IEDB + granulysin release|ELISA + ELISA measuring epitope specific granulysin release by T cells - + - + - + @@ -47567,7 +52134,7 @@ is realized in a specimen collection process. - + @@ -47581,428 +52148,558 @@ is realized in a specimen collection process. - A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|cytometric bead array - cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + intracellular material detection assay measuring epitope specific granulysin release by T cells + + A flow cytometry assay that detects epitope specific granulysin release by T cells. + IEDB + IEDB + granulysin release|intracellular staining + intracellular material detection assay measuring epitope specific granulysin release by T cells - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + - - - - An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - CCL1/TCA-3 release|ELISPOT - ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - - - - - - - - - - - - - - - - - - - - - - - + + - An enzyme-linked immunospot assay that detects interleukin-17F production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17F release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-17F production by T cells + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|cellular MHC/direct/fluorescence|1/s + fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex - + - + - + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - + - - - - An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17F release|ELISA - ELISA measuring epitope specific interleukin-17F production by T cells - - - - - - - - - - - - - - - - - - - - - - - + + - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17F release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex + + A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|cellular MHC/direct/fluorescence|nM^-1s^-1 + fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex - + - + - + - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - An enzyme-linked immunospot assay that detects interleukin-17A production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17A release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-17A production by T cells + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 + + A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM + fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 - + - - + + + + + + + + + - + - - + + + + + + + + + + + + + + + + + + + split-ubiquitin assay + Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. PMID:17513562 + + A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. + Marcus Chibucos + Philippe Rocca-Serra + url:https://en.wikipedia.org/wiki/Two-hybrid_screening + split-ubiquitin assay + + + + + + + + + + + + + + + + + + + + + - + - Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. -Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. - - - A planned process in which new information is inferred from existing information. - drawing a conclusion + + + + + + + + + + + + + + + + + + far-western blot assay + Studying protein-protein interactions via blot overlay or Far Western blot. PMID:15064457 + + An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. + Marcus Chibucos + Philippe Rocca-Serra + PMID:18079728 + far-western blot assay - + - - - - - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + - - - - A cytometric bead array assay that detects interleukin-18 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-18 production by T cells + + + + RNA protection assay + Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. PMID:11518275 + + An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. + Marcus Chibucos + Philippe Rocca-Serra + RNAse protection assay + RPA + PMID:16491611 + RNA protection assay - + - - - - - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + - - - - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells + + + + electrophoretic mobility shift assay + Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. PMID:21918373 + + An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. + Marcus Chibucos + Philippe Rocca-Serra + EMSA + band shift assay + gel mobility shift assay + gel retardation assay + gel shift assay + PMID:6269071 + electrophoretic mobility shift assay - + - - - - - + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - + + + + + + - - - - An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|ELISA - ELISA measuring epitope specific interleukin-16 production by T cells + + + + gene knock-down assay + + An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. + Marcus Chibucos + Philippe Rocca-Serra + PMID:17430206 + gene knock-down assay - + - - - - - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + - - - - An enzyme-linked immunospot assay that detects interleukin-16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-16 production by T cells + + + + + + + + + + nano-cap analysis of gene expression assay + Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846 + + A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). + Marcus Chibucos + Philippe Rocca-Serra + nano-CAGE + PMID:20543846 + nano-cap analysis of gene expression assay - + - - + + + - - + - - - - - - - - - - - - - - + + + + + + + + + + + + + - - A flow cytometry assay that detects interleukin-16 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-16 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cap analysis of gene expression assay + 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160 + + A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome + Marcus Chibucos + Philippe Rocca-Serra + CAGE + PMID:14663149 + cap analysis of gene expression assay - + - + - + @@ -48025,22 +52722,24 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17A release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells + ELISA measuring epitope specific interleukin-17A production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells. + IEDB + IEDB + IL-17A release|ELISA + ELISA measuring epitope specific interleukin-17A production by T cells - + - + - + @@ -48049,7 +52748,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -48063,371 +52762,249 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - A flow cytometry assay that detects interleukin-1 beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells - + - + - + - - - - - - - - - - - - - - - - - + + - An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells. - IEDB - IEDB - IL-1b release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells + epitope specific granulysin production by T cells + + A process of granulysin production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific granulysin production by T cells - + - + - + - - - - - - - - - - - - - - - - - + + - A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|RNA/DNA detection - detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells + epitope specific granzyme A production by T cells + + A process of granzyme A production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific granzyme A production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunospot assay that detects interleukin-12 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-12 production by T cells - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + - - - - A flow cytometry assay that detects interleukin-15 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells + + + + + + + + + + yeast 2-hybrid assay + Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. PMID:10627486 + + An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay. + Marcus Chibucos + Philippe Rocca-Serra + Y2H + url:https://en.wikipedia.org/wiki/Two-hybrid_screening + yeast 2-hybrid assay - + - - - - - + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - + + - - - - An enzyme-linked immunospot assay that detects interleukin-15 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-15 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-15 production by T cells + + + + + + + + + + Sos-recruitment assay + The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. PMID:20300944 + + A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system. + Marcus Chibucos + Philippe Rocca-Serra + SRS + PMID:9154808 + Sos-recruitment assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - + + - + - - - - - - + + + + + yeast one-hybrid assay + Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702 + + An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. + Marcus Chibucos + Philippe Rocca-Serra + Y1H + PMID:22218861 + yeast one-hybrid assay + + + + + + + + + + + + + + - - - - - - - - - + + - + + + + + + - + - Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] - - An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. - Chris Stoeckert - Jie Zheng - Venkat Malladi - ChIA-PET - ChIA-PET assay - url:http://en.wikipedia.org/wiki/ChIA-PET - chromatin interaction analysis by paired-end tag sequencing assay - - - - - - - - - Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] - - An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. - Chris Stoeckert - Jie Zheng - Venkat Malladi - DNA-PET - DNA-PET assay - PMID:23029419 - structural analysis by paired-end tag sequencing assay + bacterial one-hybrid assay + A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042 + + An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence + Marcus Chibucos + Philippe Rocca-Serra + B1H + url:http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system + bacterial one-hybrid assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -48439,7 +53016,12 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + + + + + + @@ -48450,7 +53032,10 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + + + + @@ -48464,797 +53049,718 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - - + + - - - - - - - - - + + - + + + + + + - + - Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] - - A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology. - Chris Stoeckert - Jie Zheng - Venkat Malladi - RNA-PET - RNA-PET assay - PMID:22113299 - transcript analysis by paired-end tag sequencing assay - - - - - - - - - - A transcription profiling identification objective that aims to characterize the transcription start sites of genes. - Person: Chris Stoeckert, Jie Zheng - Penn Group - transcription start site identification objective + chromosome organization assay by fluorescence in-situ hybridization + Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449 + + An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity + Marcus Chibucos + Philippe Rocca-Serra + https://github.com/obi-ontology/obi/issues/788| + chromosome organization assay by fluorescence in-situ hybridization - + - - - - - + + + + + + + + + + + + - - + + - - - - - A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. - Person: Venkat Malladi, Jie Zheng - Venkat Malladi, Jie Zheng - ENCODE project - paired-end library preparation + + + + methylation-specific polymerase chain reaction assay + Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 + + An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. + Marcus Chibucos + Philippe Rocca-Serra + MSP + PMID:8790415 + methylation-specific polymerase chain reaction assay - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - - - - - - - - - - - - - - - - + + + + + + + + + - - - - - - - - - - - - + + - - + + - - + + + amplification of intermethylated sites assay + Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 + + An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. + Marcus Chibucos + Philippe Rocca-Serra + AIMS assay + intermethylated site amplification + PMID:18987810 + amplification of intermethylated sites assay + + + + + + + + - + - - - - - - - - - + + - + + + + + + + + + + + + - + - Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] - - An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. - Chris Stoeckert - Jie Zheng - Venkat Malladi - url:http://en.wikipedia.org/wiki/DNase-Seq - DNase I hypersensitive sites sequencing assay + in-situ hybridization assay + Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 + + An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. + Marcus Chibucos + Philippe Rocca-Serra + ISH + in situ hybridization + PMID:9021518 + in-situ hybridization assay - + - - - - A sequence feature identification objective that aims to characterize the interactions between protein and RNA. - JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. - Person: Jie Zheng - Jie Zheng - protein and RNA interaction identification objective + + + + + + + + + contact representative role + + A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. + Discussed on May 7, 2012 dev call +propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? +Whether it works for communicating author in manuscript or not? +Tracker: +https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178 + Person: Chris Stoeckert + NIAID GSCID-BRC + contact representative role - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - - + + - - + + + + + + + - - - - - - - - - + + + cytochalasin-induced inhibition of actin polymerization assay + + An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). + Marcus Chibucos + Philippe Rocca-Serra + cytochalasin-induced inhibition of actin polymerization assay + + + + + + + + + molecular function identification objective + + is an objective specification which aims to discover molecular function realized by a molecular entity + PERSON:Philippe Rocca-Serra + OBI group + molecular function identification objective + + + + + + + + + cellular structure feature identification objective + + is an objective specification which aims to discover cellular structure properties + PERSON:Philippe Rocca-Serra + OBI group + cellular structure feature identification objective + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] + in vivo assay measuring B cell epitope specific protection from fertility - An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). - Chris Stoeckert - Jie Zheng - Venkat Malladi - RIP-seq - RIP-seq assay - PMID:21172659 - RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + protection from fertility|in vivo assay + in vivo assay measuring B cell epitope specific protection from fertility - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + - - + + in vivo assay measuring B cell epitope specific tolerance induction + + An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + tolerance|in vivo assay + in vivo assay measuring B cell epitope specific tolerance induction + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + - + - - - + + + - - + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] + + in vivo assay measuring B cell epitope specific induction of hypersensitivity - An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. - Chris Stoeckert - Jie Zheng - Venkat Malladi - CLIP-seq - CLIP-seq assay - HITS-CLIP - PMID:18978773 - cross-linking immunoprecipitation high-throughput sequencing assay + An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + hypersensitivity|in vivo assay + in vivo assay measuring B cell epitope specific induction of hypersensitivity - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - + - - - + + + - - + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] + + assay measuring epitope specific immune complex formation - An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. - Chris Stoeckert - Jie Zheng - Venkat Malladi - FAIRE-seq - FAIRE-seq assay - url:http://en.wikipedia.org/wiki/FAIRE-Seq - formaldehyde-assisted isolation of regulatory elements assay + A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + agglutination|biological activity + assay measuring epitope specific immune complex formation - + - - - + + + - + + + + + - - - - - - - + + + + + + + + - - - - - - - - - - - + - - - + + + - - + + + + + + + + + + + + - - + + - + - - - + + + - - + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] - - An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. - Chris Stoeckert - Jie Zheng - Venkat Malladi - MRE-seq - MRE-seq assay - PMID:20613842 - methylation-sensitive restriction enzyme sequencing assay - - - - - - - - - - - - - - - - - - - - - Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174] + + in vivo assay measuring B cell epitope specific protection based on survival - A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. - Chris Stoeckert - Jie Zheng - Venkat Malladi - RRBS - RRBS assay - reduced representation bisulfite-seq - PMC:1258174 - reduced representation bisulfite sequencing assay + An in vivo assay measuring B cell epitope specific protection from other challenge using survival. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + survival from challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection based on survival - + - - - + + + - + + + + + - - - + + + - - + + + + + + + + + + + + - - + + - - + + + + + + + + + + + + - - - - - - - - Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. + + in vivo assay measuring B cell epitope specific treatment of disease - A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Shotgun bisulfite sequencing - WGBS - WGSBS - whole genome bisulfite sequencing - whole-genome shotgun bisulfite sequencing - PMID:18278030 - shotgun bisulfite-seq assay + An efficacy of B cell epitope intervention experiment that detects a decrease in disease. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + decreased disease|in vivo assay + in vivo assay measuring B cell epitope specific treatment of disease - + - - - + + + - + - - - + + + - - + + + + + + + + + + + + - - + + - - + + + + + + + + + + + + - + + assay measuring B cell epitope specific in vivo activity + + A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + in vivo activity|biological activity + assay measuring B cell epitope specific in vivo activity + + + + + + + + @@ -49266,7 +53772,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -49277,7 +53783,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -49291,24 +53797,94 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - - - - - - - - + + + + + + + + + + + + + antibody cross-blocking assay + Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. + + A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. + IEDB + antibody inhibition of antibody binding + IEDB + antibody cross-blocking assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + immunoprecipitation assay + Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. + + An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. + IEDB + IEDB + immunoprecipitation assay + + + + + + + + - + - - + + + + + @@ -49317,4794 +53893,5628 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + - - + + + + + + + - Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] + antigen inhibition assay measuring binding of a B cell epitope:antibody complex - An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. - Chris Stoeckert - Jie Zheng - Venkat Malladi - RAMPAGE - PMID:22936248 - RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay + A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|inhibition by antigen + antigen inhibition assay measuring binding of a B cell epitope:antibody complex - + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + immunoglobulin binding to epitope + Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus - A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. - PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Penn Group - assay array + a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). + PERSON: Bjoern Peters, Randi Vita + IEDB + immunoglobulin binding to epitope - + - - - + + - + + - - + + - + - - + + - + - - - - - - - - secondary cultured cell + + assay measuring qualitative binding of a B cell epitope:antibody complex - A cultured cell that has been passaged or derives from a cell that has been passaged in culture. - The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. - Person: Matthew Brush - PERSON: Matthew Brush - A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. - secondary cultured cell + An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output. + IEDB + IEDB + qualitative binding|binding assay + assay measuring qualitative binding of a B cell epitope:antibody complex - + - - - - - - - - - establishing cell line + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific activation of additional immune response in vitro - a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). - 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. - Person: Matthew Brush - PERSON:Matthew Brush - establishing cell line + A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. + IEDB + IEDB + secondary in vitro activity|biological activity + assay measuring epitope specific activation of additional immune response in vitro - + - - + + - + - - - - + + + + + + + - - A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. - MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. - -Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion). - genomic material - hereditary genetic material - OBI developer calls, March 4 2013 and March 11 2013 - Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material. - -Qualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. - -Non-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells). - - genetic material - - - - - - - - - - + + + + + + + + + + + + + assay measuring epitope specific antigen inhibition of antibody activity - An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. - PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi - http://www.illumina.com/technology/beadarray_technology.ilmn - Illumina BeadChip + A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. + IEDB + IEDB + antibody activity inhibition|biological activity + assay measuring epitope specific antigen inhibition of antibody activity - + - + - + - + - - - + + + - - - - - - - - - - - - - - - - - - - - - - + + - - + + + assay measuring biological activity resulting from B cell epitope:antibody binding - A BeadChip made for an analyte assay that generates information about DNA methylation. - PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Penn Group - Illumina methylation BeadChip + A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope. + IEDB + IEDB + biological activity|any method + assay measuring biological activity resulting from B cell epitope:antibody binding - + - - - - - - - - - - A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. - Anna Maria Masci - http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg - LSRFortessa X-20 + + + immunoglobulin mediated histamine release + + The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. + 4/26/12, BP: We want to import this from GO, which currently only has IgE mediated histamine release. We have requested the term, but need to use this as a placeholder in the meanwhile. + PERSON: Bjoern Peters, Randi Vita + IEDB + immunoglobulin mediated histamine release - + - - - - - - + + + + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). - PRS/AGB: -changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. - - Alejandra Gonzalez-Beltran - PERSON: Jie Zheng, Chris Stoeckert - Philippe Rocca-Serra - NIAID GSCID-BRC metadata working group - NIAID GSCID-BRC - sequence assembly process - - - - - - - - - - - - - - - - - - - - - Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. -PMID: 23587118. see table2 - - a data item that is the number of times that a given process failed, as an integer - Alejandra Gonzalez-Beltran - Philippe Rocca-Serra - PRS, AGB - number of errors + + + + + + + + + + + + + + + + + + + + + + assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + A B cell epitope binding constant determination assay that measures the dissociation constant KD. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|binding assay|nM + assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - + - - - - - - - - - + + + + + + + + + + + + - - + + - - - - - - Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. -PMID: 23587118. -"However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads" - - random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation - Alejandra Gonzalez-Beltran - Philippe Rocca-Serra - PRS, AGB - random access memory size + + + + + + assay measuring a binding constant of a B cell epitope:antibody complex + + A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + binding constant|binding assay + assay measuring a binding constant of a B cell epitope:antibody complex - + - - - cultured immune cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from challenge - a cultured cell population comprised of a single type of immune system cell - MHB 3-5-13: created as a (temporary) organizational class to organize IEDB immune cultured cell population types. These were all previously labled as 'cell cultures' - and relabeld here as 'cultured cell populations' since a CLO alignment outcome was to use the term 'cell culture' to refer to cultured cells + media. Consult with BP as to whether this organizational class is useful and if so, how to define it. Also check whether the intent was to represent cell populations rather than cell cultures. - PERSON:Matthew Brush - immune cell culture sample - PERSON:Matthew Brush - cultured immune cell population + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + protection from challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection from challenge - + - - - - - - - - - - - - - - - - - - - - - - cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific disease exacerbation - A material entity comprised of cultured cells and the media in which they are being propagated or stored. - PERSON:Matthew Brush - OBI-CLO Alignment Working Group (Spring 2013) - A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored. - cell culture + An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + disease exacerbation|in vivo assay + in vivo assay measuring B cell epitope specific disease exacerbation - + - - - - Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location - Alejandra Gonzalez-Beltran - Philippe Rocca-Serra - RAM - http://en.wikipedia.org/wiki/RAM -last accessed: 2013-12-02 - random access memory + + + obsolete B cell epitope direct binding assay + + A direct binding assay using a assay + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + + direct binding assay + obsolete B cell epitope direct binding assay + true - - - - - - - - - - - establishing primary cell culture - Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages. -Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488 + -When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium. - - an establishing cell culture process whereby cells explanted directly from an organismal source or specimen, and placed in culture for maintenance or propagation as a primary cell culture - PERSON: Matthew Brush - Cells are originally plated at a certain concentration referred to as seeding density. Upon a first passage this primary culture becomes a secondary cell culture that can be propagated to become a stable and homogneous cell line. This class covers establishment of primary cultures from any native cell - 'in vivo' cells isolated from some multicellular organism, or 'in environment' unicellular organisms isolated from some natural environment. - establishing primary cell culture + + + + + + + + + + + + + B cell epitope specific opsonization + + opsonization resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific opsonization - + - + - + - - + + - - - - - - - - - A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. - 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. - PERSON:Matthew Brush - PERSON:Matthew Brush - (copied from ReO) -Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. + B cell epitope specific immunoglobulin-mediated neutralization + + immunoglobulin-mediated neutralization resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific immunoglobulin-mediated neutralization + + -Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. -In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). - reagent + + + + + obsolete B cell epitope competitive binding assay + + A competitive inhibition of binding assay using a assay + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + + competitive binding assay + obsolete B cell epitope competitive binding assay + true - + - + - + - - + + - - An organization that is the affiliation of the principal investigator providing the specimens for the investigation - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sample Provider PI's Institution - NIAID GSCID-BRC - organization of specimen provider principal investigator + B cell epitope specific complement-dependent cytotoxicity + + complement-dependent cytotoxicity resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific complement-dependent cytotoxicity - + - + - + - - + + - - An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Bioinformatics Resource Center Contact's Institution - NIAID GSCID-BRC - organization of Bioinformatics Resource Center contact person + B cell epitope specific antibody-dependent cellular cytotoxicity + + antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific antibody-dependent cellular cytotoxicity - + - - - - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - - - - + + - - - - - - Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome. + + + + + + + + + + + + + + + assay measuring the on rate [kon] of a B cell epitope:antibody complex - A plan specification which specifies the type of material that will be assayed in an investigation. - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Target Material - NIAID GSCID-BRC - target material in specimen specification + A B cell epitope binding constant determination assay that measures the on rate. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|binding assay|M^-1s^-1 + assay measuring the on rate [kon] of a B cell epitope:antibody complex - + - + - + - - + + - - + + + + + + + + + + + + + + + + + assay measuring the association constant [KA] of a B cell epitope:antibody complex - A person who is the contact representative of a Bioinformatics Resource Center - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Bioinformatics Resource Center Contact Name - NIAID GSCID-BRC - Bioinformatics Resource Center contact person + A B cell epitope binding constant determination assay that measures the association constant KA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|binding assay|1/nM + assay measuring the association constant [KA] of a B cell epitope:antibody complex - + - - - - - - - - - - - - - - - - - - - - Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic. - - A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sample Scope - NIAID GSCID-BRC - specimen-based scope of investigation specification + + + + + + + + + + B cell epitope specific immune complex formation + + immune complex formation resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific immune complex formation - + - + - + - + + + + + - - - - - - - - - - - - - - - - - - - + + + + + 3D molecular structure determination assay of an antigen:antibody complex - An organization that provides a service to store and distribute specimens - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Specimen Repository - NIAID GSCID-BRC - specimen repository organization + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|any method + 3D molecular structure determination assay of an antigen:antibody complex - + - + - + - - + + - - An email address of the person who is contact representative of a Bioinformatics Resource Center - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Bioinformatics Resource Center Contact's email - NIAID GSCID-BRC - email address of Bioinformatics Resource Center contact person + B cell epitope specific hypersensitivity + + hypersensitivity resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific hypersensitivity - + - + - + - - + + - - + + + + + + + + + + + + + + + + + assay measuring the off rate [koff] of a B cell epitope:antibody complex - A person who is the contact representative at the sequencing facility - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sequencing Facility Contact Name - NIAID GSCID-BRC - sequencing facility contact person + A B cell epitope binding constant determination assay that measures the off rate. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|binding assay|1/s + assay measuring the off rate [koff] of a B cell epitope:antibody complex - + - + - + - - + + - - + + + + + + + + viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex - A person who is a principal investigator and provides the specimen - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sample Provider Principal Investigator (PI) Name - NIAID GSCID-BRC - specimen provider principal investigator + A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding| hemagglutination inhibition + viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex - + - + - + - - + + - - An email address of the person collecting the specimen - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Specimen Collector's email - NIAID GSCID-BRC - email address of specimen collector + B cell epitope specific histamine secretion mediated by immunoglobulin + + histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific histamine secretion mediated by immunoglobulin - + - + - + - + + + + + - - - - - - - - - + + + + + quenching assay measuring binding of a B cell epitope:antibody complex - An organization that provides sequence determination service - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sequencing Facility - NIAID GSCID-BRC - sequencing facility organization + A fluorescence quenching assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|quenching + quenching assay measuring binding of a B cell epitope:antibody complex - + - - - - - - - - - - - - - - - + + + + + + + + + + + + - - - - - - - - - + + - - - - - - Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype + + + + + + + + + + + + + + + RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex - An objective specification which indicates the type of data that will be generated and submitted to a database. - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Project Objectives - NIAID GSCID-BRC - specification of data to be generated in an investigation + A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|radio immuno assay (RIA)|nM + RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex - + - + - + - - + + + + + + + + + + + + + + + + + + + + + ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex - An organization that is the affiliation of the person collecting the specimen - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Specimen Collector's Institution - NIAID GSCID-BRC - organization of specimen collector + An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|ELISA|nM + ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex - + - + - + - - + + + + + + + + + + + + + + + + + + + + + quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - An email address of the contact representative at the sequencing facility - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sequencing Facility Contact's email - NIAID GSCID-BRC - email address of sequencing facility contact person + A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|quenching|nM + quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - + - + - + - - + + + + + + + + + + + + + + + + + + + + + surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex - A person who collects the specimen - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Specimen Collector Name - NIAID GSCID-BRC - specimen collector - - - - - - - - - - - - - - - - - - - - - Some examples of Project Method are Sequence, Array, Mass Spectrometry - - A plan specification which indicates the assay type used to obtain data. - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Project Method - NIAID GSCID-BRC - investigation assay specification + A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|surface plasmon resonance (SPR)|1/nM + surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex - + - + - + - - + + + + + + + + + + + + + + + + + + + + + surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - An organization that is the affiliation of the contact representative at the sequencing facility - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sequencing Facility Contact's Institution - NIAID GSCID-BRC - organization of sequencing facility contact person + A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|surface plasmon resonance (SPR)|nM + surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - + - + - + - + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex - A textual entity that is about any of the aspects of an investigation worth noting - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Comments - NIAID GSCID-BRC - comment on investigation + A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|quenching|1/nM + quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex - + - - - - - - - - - - - - - - - + + + + + + + + + + + + - - + + + + + + + - - - - - - - - - - - - + + - - - - - - Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey + + + + + + calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex - A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Target Capture - NIAID GSCID-BRC - target capture specification + A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|calorimetry|1/nM + calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex - + - + - + - + + + + + - - - - - - - - - + + + + + + + + + + + + + + calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A specimen identifier which is assigned by a specimen repository - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Specimen Repository Sample ID - NIAID GSCID-BRC - specimen identifier assigned by specimen repository + A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|calorimetry|nM + calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - + - + - + - + + + + + - - - - - - - - - + + + + + + + + + + + + + + ELISA measuring the association constant [KA] of a B cell epitope:antibody complex - A specimen identifier which is assigned by a sequencing facility - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sample ID - Sequencing Facility - NIAID GSCID-BRC - specimen identifier assigned by sequencing facility + An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|ELISA|1/nM + ELISA measuring the association constant [KA] of a B cell epitope:antibody complex - + - + - + - + + + + + - - - - - - - - - + + + + - - - - - - - - - + + + + + RIA measuring the association constant [KA] of a B cell epitope:antibody complex - A sample preparation for assay that preparation of nucleic acids for a sequencing assay - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Nucleic Acid Preparation Method - NIAID GSCID-BRC - sample preparation for sequencing assay + A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|radio immuno assay (RIA)|1/nM + RIA measuring the association constant [KA] of a B cell epitope:antibody complex - + - + + + obsolete B cell epitope specific X-ray crystallography assay + + A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + + + X-ray crystallography [Ã…] + obsolete B cell epitope specific X-ray crystallography assay + true + + + + + + + - + - - + + + + + + + + + + + + + + + + + + + + + X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex - An email address of the principal investigator providing the specimens for the investigation - PERSON: Chris Stoeckert, Jie Zheng - NIAID GSCID-BRC metadata working group - Sample Provider PI's email - NIAID GSCID-BRC - email address of specimen provider principal investigator + A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|x-ray crystallography|angstroms + X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex - + - + - + - - + + + + + + + + + + + + + + + + + + + + + surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex - A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. - Person: Jie Zheng - Adpated from 'DNA sequencing service' - NIAID GSCID-BRC - sequencing service + A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|surface plasmon resonance (SPR)|1/s + surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex - + - - - - - - - - - - - - - - - - - - - - - secondary cultured cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex - A cultured cell population that is derived through one or more passages in culture. - The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. - PERSON:Matthew Brush - secondary cell culture sample - PERSON:Matthew Brush - The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. - secondary cultured cell population - - - - - - - - - - - - - - - cancer cell line - - An immortal cell line derived from a transformed cell that was part of a malignant tumor. - cancer cell line - - - - - - - - - - - - - - - immortalizing cell line transformation - - a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture - immortalizing cell line transformation + A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|quenching|1/s + quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex - + - - - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - An information content entity that expresses an assertion that is intended to be tested. - In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. - - Group:2013 Philly Workshop group - hypothesis - Group:2013 Philly Workshop group - testable hypothesis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex + + A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|surface plasmon resonance (SPR)|M^-1s^-1 + surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex - + - - - - - - - - - - - - - - - The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. -The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". - - An information content entity that is inferred from data. - In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. - Group:2013 Philly Workshop group - Group:2013 Philly Workshop group - conclusion based on data + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex + + A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|quenching|M^-1s^-1 + quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex - + - - - - - - - - - primary cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells - A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. - PERSON:Matthew Brush - OBI-CLO Alignment Working Group (Spring 2013) - primary cell culture + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells - + - - - - - - - - - cell line culture + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells - A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored. - PERSON:Matthew Brush - OBI-CLO Alignment Working Group (Spring 2013) - A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored. - cell line culture + A flow cytometry assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells - + - - - cell freezing medium + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells - A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. - PERSON: Matthew Brush - cell freezing medium + An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells - - - - - - - - - - - Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. -PMID: 23587118. + -See Table 4 - - computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency. - - Alejandra Gonzalez-Beltran - Philippe Rocca-Serra - computation run time datum - PRS,AGB - computation run time + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells - + - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells - A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. - Chris Stoeckert, Jie Zheng - LMA - MLPA - Multiplex ligation-dependent probe amplification - web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification -Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - multiplex ligation-mediated amplification + A cytometric bead array assay that detects interleukin-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1a release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + ELISPOT assay measuring epitope specific interferon-beta production by T cells + + An enzyme-linked immunospot assay that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|ELISPOT + ELISPOT assay measuring epitope specific interferon-beta production by T cells + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells + + A flow cytometry assay that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|ICS + intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells + + + + + + + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] + + intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells - An assay which quantifies the timing of DNA replication as a function of genome position using array technology. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Repli-chip - Repli-chip assay - PMID:18842067 - DNA replication timing by array assay + A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + G-CSF release|ICS + intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interferon-beta production by T cells - A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. - Chris Stoeckert, Jie Zheng - Group: Penn Group - DNA replication identification objective + An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNb release|ELISA + ELISA measuring epitope specific interferon-beta production by T cells - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells - A molecular feature identification objective that aims to determine spatial organization of chromatin. - Chris Stoeckert, Jie Zheng - Group: Penn Group - chromosome conformation identification objective + A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + G-CSF release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells + + An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + G-CSF release|ELISPOT + ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells + + + + + + + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] + + cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). - Chris Stoeckert - Jie Zheng - Venkat Malladi - RIP-chip - RIP-chip assay - PMID:21125495 - RNA-binding protein immunoprecipitation array profiling assay + A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|cytometric bead array + cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - + - - - + + + selection criterion + rats should be aged between 6 and 8 weeks and weight between 180-250grams + + A directive information entity which defines and states a principle of standard by which selection process may take place. + Person: Philippe Rocca-Serra + selection rule + OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ + selection criterion + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + + An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|ELISPOT + ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells + + + + + + + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - An assay that measures the organization of chromosomes at the genome-wide scale. - Chris Stoeckert - Jie Zheng - Venkat Malladi - 5C - 5C assay - PMID:16954542 - Carbon-copy chromosome conformation capture assay + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL9/MIG release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + + An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells. + IEDB + IEDB + CCL4/MIP-1b release|ELISPOT + ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL12/SDF-1 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL13/BLC release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + + + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139_�_144. [PMID:19966280] + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Repli-seq - Repli-seq assay - PMID:19966280 - DNA replication timing by sequencing assay + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL16 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells - An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). - Chris Stoeckert - Jie Zheng - Venkat Malladi - PMID:21125495 - RNA-binding protein immunoprecipitation tiling array profiling assay + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL21/SLC release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL22/MDC release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767 + + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. - Chris Stoeckert - Jie Zheng - Venkat Malladi - miRNA-HTS - miRNA-seq - microRNA-seq - microRNA-seq assay - url:http://www.ebi.ac.uk/efo/EFO_0002896 - microRNA profiling by high throughput sequencing assay + A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL4/MIP-1b release|cytometric bead array + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells. + IEDB + IEDB + CCL4/MIP-1b release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells + + + + + + + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] + + detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells - A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. - Chris Stoeckert - Jie Zheng - Venkat Malladi - PMID:3462691 - protein sequencing by tandem mass spectrometry assay + A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL19/MIP-3b release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells + + + + + + + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - + + intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + + A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|ICS + intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] + specimen collector role - An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease - Chris Stoeckert - Jie Zheng - Venkat Malladi - MNase-seq - MNase-seq assay - PMID:17038564 - micrococcal nuclease digestion followed by high throughput sequencing assay + An Investigation agent role borne by a person or organization which +is realized in a specimen collection process. + Person: Jie Zheng, Chris Stoeckert + Penn Group + NIAID GSCID-BRC + specimen collector role - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] + + intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells - A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site - Bjoern Peters - Chris Stoeckert - Jie Zheng - Venkat Malladi - ChIP-exo assay - PMID:22153082 - chromatin immunoprecipitation with exonuclease sequencing assay + A flow cytometry assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|ICS + intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - + + ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells - A transcription profiling assay that quantifies the microRNA species within a biological sample. - Chris Stoeckert - Jie Zheng - Venkat Malladi - miRNA expression assay - microRNA expression assay - PMID: 23382819 - microRNA profiling assay + An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|ELISPOT + ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells - + - + - - - + + + - - + + + + + + + + + + + + + + + + + - - + + - - PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. - - A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. - this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) - Person: Philippe Rocca-Serra - selection process - OBI - selection + assay measuring epitope specific interleukin-17F production by T cells + + An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17F release|biological activity + assay measuring epitope specific interleukin-17F production by T cells - + - - - - - - - - - - - - - - - A value specification that specifies the mass of some thing. - PERSON:Bjoern Peters - mass value specification - - - - - - - - - - A value specification that is specifies one category out of a fixed number of nominal categories - PERSON:Bjoern Peters - categorical value specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific interleukin-17A production by T cells + + An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17A release|biological activity + assay measuring epitope specific interleukin-17A production by T cells - + - - - - - - 1 - - - - - - 1 - - - - A value specification that consists of two parts: a numeral and a unit label - PERSON:Bjoern Peters - scalar value specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL21/SLC release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells - + - - - - - - - - - + + + + + + + + - + - + - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - A planned process in which predicted values for some thing are compared to measured values for that thing. - comparing prediction to measurement + + + + + + assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL19/MIP-3b release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells - + - - - The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. - - An information content entity that specifies a value within a classification scheme or on a quantitative scale. - This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. - PERSON:Bjoern Peters - value specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells. + IEDB + IEDB + CXCL12/SDF-1 release|biological activity + assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - + - - - - - - - - - - - - - - - + + + + + + + + - - - - - - - + + + + + + + + + + + + - - - - - - - an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. - PERSON:Bjoern Peters - predicted value + + + + + + assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL22/MDC release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - - A predicted value where the prediction specifies the mass of some thing. - PERSON:Bjoern Peters - predicted mass value + assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL16 release|biological activity + assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells - + - + - - - - - + - - + + + + + + + + + + + + + + + + + - molecular-labeled material - - a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay - PERSON:Matthew Brush - OBI developer call, 3-12-12 - molecular-labeled material + assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL13/BLC release|biological activity + assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells - - - - - - - - - - - - - - - - - Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. -PMID: 23587118. + -"The genome coverage increased from 81.16% to 93.91%" - - A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%. - Alejandra Gonzalez-Beltran - Philippe Rocca-Serra - A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. -Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. -PMID: 22510764 - genome coverage + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|ELISPOT + ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells - - - - - - - - - - - - - - - - - - - - - - - Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. -PMID: 23587118. + -"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - - the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly - Alejandra Gonzalez-Beltran - Philippe Rocca-Serra - weighted median item size - adapted from: -"http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" -(from table 7) -and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html" - N50 + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + + A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|cytometric bead array + cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - + - - - - - - - - - + + + + + + + + - - + + + + + + + + + + + + - - - - - - Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. -PMID: 23587118. - -"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - - N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. - Alejandra Gonzalez-Beltran - Philippe Rocca-Serra - adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html - contig N50 + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - + - - - - An organization that provides funding support for projects such as investigations. - PERSON: Jie Zheng, Chris Stoeckert - funding organization - NIAID GSCID-BRC metadata working group - NIAID GSCID-BRC - grant agency - 'funding organization' -http://vivoweb.org/ontology/core#FundingOrganization - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. - PERSON: Jie Zheng, Chris Stoeckert - WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29 - NIAID GSCID-BRC - software pipeline + A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|ICS + intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - + - - - - - - + + + + + - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - + + + + ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. - PERSON: Jie Zheng, Chris Stoeckert - NIAID GSCID-BRC metadata working group - NIAID GSCID-BRC - sequence annotation + An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL2/MCP-1 release|ELISPOT + ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells - + - - - - - - - - - + + + + + + + + - - + + + + + + + + + + + + - - - - - - Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. -PMID: 23587118. - -"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" - - N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information - Alejandra Gonzalez-Beltran - Philippe Rocca-Serra - adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html - scaffold N50 + + + + + + intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + + A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|ICS + intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - + - - + + - + - - + + + + + + + + + + + + + + + + + - - SP6 promoter, forward primer (SP6 TTTAGGTGACACTATAG) - - A short oligonucleotide complementary to target DNA (5'->3' on plus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. - Philippe Rocca-Serra - 5' primer - forward primer - sense primer - adapted from http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p - forward PCR primer + + ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells + + An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL9/MIP-1g release|ELISPOT + ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells - + - + - - - - - - + - - + + + + + + + + + + + + + + + + + - + cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells - A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. - PERSON: Jie Zheng, Chris Stoeckert - NIAID GSCID-BRC metadata working group - annotation provider - NIAID GSCID-BRC - sequence annotation provider + A cytometric bead array assay that detects vascular endothelial growth factor production by T cells. + IEDB + IEDB + VEGF release|cytometric bead array + cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - A textual entity that is used to denote a sequence assembly. - PERSON: Jie Zheng, Chris Stoeckert - NIAID GSCID-BRC metadata working group - assembly name - NIAID GSCID-BRC - sequence assembly name + A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells. + IEDB + IEDB + TNF release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific RANTES production by T cells - A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. - PERSON: Jie Zheng, Chris Stoeckert - NIAID GSCID-BRC metadata working group - NIAID GSCID-BRC - sequence annotation reporting role + A flow cytometry assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|ICS + intracellular cytokine staining assay measuring epitope specific RANTES production by T cells - + - - + + - + - - + + + + + + + + + + + + + + + + + - - - 5' end of luciferase, reverse primer (LucNrev CCTTATGCAGTTGCTCTCC) - - A short oligonucleotide complementary to target DNA (5'->3' on minus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. - Philippe Rocca-Serra - 3' primer - antisense primer - reverse primer - adapted from "http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p" - reverse PCR primer - - - - - - - - + + ELISPOT assay measuring epitope specific RANTES production by T cells - A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. - Person: Mathias Brochhausen, Jie Zheng - WEB: http://en.wikipedia.org/wiki/Flash_freezing - flash freezing + An enzyme-linked immunospot assay that detects RANTES production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL5/RANTES release|ELISPOT + ELISPOT assay measuring epitope specific RANTES production by T cells - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific lymphotoxin A production by T cells - A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities. - Person: Mathias Brochhausen, Jie Zheng - Mathias Brochhausen - freezing + An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells. + IEDB + IEDB + lymphotoxin A/TNFb release|ELISPOT + ELISPOT assay measuring epitope specific lymphotoxin A production by T cells - + - + - - - + + + + - + - + - - - - - - - + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL3/MIP-1a release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells + + + + + + + + + + + + + + - + + - - - - - - + + - - - - - - - - - - - - - - - - PMID: 6379641 - - An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed - Bjoern Peters - Philippe Rocca-Serra - chromatin immunoprecipitation assay - url:https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation - ChIP assay + cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells + + A cytometric bead array assay that detects lymphotoxin A production by T cells. + IEDB + IEDB + lymphotoxin A/TNFb release|cytometric bead array + cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells - + - - - competitive binding reference ligand role - The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion. - A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. - Bjoern Peters, Randi Vita, James A. Overton - Bjoern Peters - competitive binding reference ligand role + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells. + IEDB + IEDB + lymphotoxin A/TNFb release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells - + - - - - - - - - - - - - - - - - - - - - - - http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html - - An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation - Philippe Rocca-Serra - http://sourceforge.net/p/obi/obi-terms/707/ - assay using chromatin immunoprecipitation - - - - - - - + - + - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - + ELISPOT assay measuring epitope specific IP-10 production by T cells - A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. - Person: Jie Zheng - MO_734 hardware_variation_design - hardware testing design + An enzyme-linked immunospot assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|ELISPOT + ELISPOT assay measuring epitope specific IP-10 production by T cells - + - - - systematic review study design - Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ - The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells - A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. - PERSON: Bill Hogan - systematic review study design - - - - - - - - - - - - - - - - - - - - - http://www.illumina.com/technology/multiplexing_sequencing_assay.ilmn - - A planned process which consists in running a set of samples as a pool on a sequencing instrument, while retaining the ability to associate individual results to each of the individual input samples through the use of a ligated oligonucleotide (the "multiplex identifier sequence"). This oligonucleotide is introduced during the sequence library preparation, and is unique to and specific for all library fragments derived from each sample in a sample pool. - Dan Berrios - PERSON:Philippe Rocca-Serra - OBI - multiplexed nucleotide library sequencing + A flow cytometry assay that detects IP-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CXCL10/IP-10 release|ICS + intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells - + - + - + - + + + + + + + + + + + - - - - - PMID:20679230 - PMID:25367129 - - An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. - Philippe Rocca-Serra - environmental gene survey - targeted gene survey - targeted gene survey DNA barcoding - OBI - taxonomic diversity assessment by targeted gene survey - - - - - - - - - https://www.neb.com/protocols/1/01/01/taq-dna-polymerase-with-standard-taq-buffer-m0273 - - a PCR program is a plan specification which is executed during a polymerase chain reaction (PCR) by a thermocycler instrument that will iterate through the changes in temperature and duration of each of the annealing, denaturation, elongation steps for as many times as specified by the program. - PERSON:Philippe Rocca-Serra - OBI - PCR program - - - - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/25367129 - -"performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene) - - is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey - PERSON:Philippe Rocca-Serra - PRS for OBI - target gene - target gene specification - - - - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/23335919 - -"performing a profiling of microbial phylogenetic composition using massively-parallel pyrotag sequencing targeting the V9 hypervariable region (used as target subfragment) of the 18S ribosomal RNA (rRNA) gene (used as target gene) - - is a directive information specifying a genomic region, possibly located in a coding genomic region, which is the focus of a planned process such as an assay, for instance in a environmental gene survey - PERSON:Philippe Rocca-Serra - PRS for OBI - target subfragment - target subfragment specification - - - - - - - - - decision-theoretic analysis objective + ELISPOT assay measuring epitope specific interleukin-9 production by T cells - An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. - The best action to take is typically defined as the one that maximizes expected utility. - PERSON: Bill Hogan - decision analysis objective - PERSON: Bill Hogan - decision-theoretic analysis objective + An enzyme-linked immunospot assay that detects interleukin-9 production by T cells. + IEDB + IEDB + IL-9 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-9 production by T cells - + - + - + - - + + + + + + + + + + + + + + + + + - decision analysis study design + intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells - a study design that has a decision analysis objective specification as part - PERSON: Bill Hogan - PERSON: Bill Hogan - decision analysis study design - - - - - - - - - - - - - - - - is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to separate all reads belonging to a given single sample following the sequencing of a multiplexed library - PERSON: Philippe Rocca-Serra - PRS for OBI - sequence library data demultiplexing - - - - - - - - - - - - - - - - - - - - - - We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. in http://www.ncbi.nlm.nih.gov/pubmed/22574170 - - A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library - PERSON:Philippe Rocca-Serra - OBI - multiplexing sequence identifier - - - - - - - - - - - - - - - - - - - - - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1610290/ - - Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism. - - PERSON:Philippe Rocca-Serra - PRS for OBI - operational taxonomic unit matrix - - - - - - - - - - biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level - PERSON:Philippe Rocca-Serra - PRS for OBI - biodiversity assessment objective - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/24997861 - -Nat Methods. 2014 Aug;11(8):834-40. doi: 10.1038/nmeth.3022. Epub 2014 Jul 6. -Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run. - PERSON:Philippe Rocca-Serra - DNA-barcoded sequencing library - PRS for OBI - multiplexed sequencing library - - - - - - - - - Ion 316 Chip v2 - An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. - Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ - PERSON: Sagar Jain - Ion 316 Chip - Ion PGM 316 Chip - Ion PGM 316 Chip v2 - http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html - Ion 316 Chip v2 - - - - - - - - - Ion 318 Chip v2 - An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. - Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ - PERSON: Sagar Jain - Ion 318 Chip - Ion PGM 318 Chip - Ion PGM 318 Chip v2 - http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html - Ion 318 Chip v2 - - - - - - - - - ion semiconductor chip - An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface. - Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/ - PERSON: Sagar Jain - ion chip - ion integrated circuit - ion semiconductor - http://www.thefreedictionary.com/Semiconductor+chip - ion semiconductor chip - - - - - - - - - Ion 314 Chip v2 - An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb. - Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/ - PERSON: Sagar Jain - Ion 314 Chip - Ion PGM 314 Chip - Ion PGM 314 Chip v2 - http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html - Ion 314 Chip v2 + A flow cytometry assay that detects interleukin-9 production by T cells. + IEDB + IEDB + IL-9 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface. - A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. - IEDB - IEDB - hydrogen/deuterium exchange footprinting assay + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells. + IEDB + IEDB + IL-9 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells - + - + - - - + + + + - + - + - - + + + + + + + + ELISPOT assay measuring epitope specific interleukin-8 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-8 production by T cells. + IEDB + IEDB + IL-8 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-8 production by T cells + + + + + + + + + + + + + + - + - + - - + + - - + + - An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. - An assay that counts and/or measures characteristics of cells. - IEDB - IEDB - cytometry assay + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells. + IEDB + IEDB + IL-8 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells - + - - - + + + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. - IEDB - IEDB - immunoblot assay - - - - - - - - - - - - - - - - - - - - - - A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. - IEDB - IEDB - fluorescence quenching binding assay + + ELISPOT assay measuring epitope specific interleukin-3 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-3 production by T cells - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + + + + + + + + + + + - - Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival. - An assay in which the effect of a targeted process (the intervention) on an organism is tested. - The intervention in an experiment should be modeled accordingly to the intevention carried out in a human cllinical trial, which is currently modeled as 'study intervention'. This touches the boundaries of study vs. assay. - IEDB - IEDB - in vivo intervention experiment - - - - - - - - - Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide. - An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. - Should have data about disease severity as readout; could just use disease for now - IEDB - IEDB - disease exacerbation in vivo intervention experiment - - - - - - - - - Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide. - An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. - should have challenge as intervention - IEDB - IEDB - protection from challenge in vivo intervention experiment - - - - - - - - - Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide. - An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. - should have tolerance induction as intervention - IEDB - IEDB - tolerance induction intervention experiment - - - - - - - - - Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals. - An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. - should have treatment as intervention - IEDB - IEDB - treatment intervention experiment + + ELISA measuring epitope specific interleukin-7 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-7 release|ELISA + ELISA measuring epitope specific interleukin-7 production by T cells - + - + - - - + + + + - + - + - - + + - - - - - - + + - Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray. - An analyte assay where binding of the analyte to immobilized matrix is measured. - IEDB - IEDB - microarray assay + ELISPOT assay measuring epitope specific interleukin-7 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-7 production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - + - + - - + + - - - - - - + + - Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. - An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. - IEDB - IEDB - immunohistochemistry + intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells + + A flow cytometry assay that detects interleukin-7 production by T cells. + IEDB + IEDB + IL-7 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells - + - + - - - - - + - - - - - - - - - - + + + + + + + + + + + - A MHC binding constant determination assay measuring equilibrium association constant (KA). - IEDB - IEDB - association constant KA|binding assay|1/M - assay measuring the association constant [KA] of a MHC:ligand complex + intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells + + A flow cytometry assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells - + - + - - - - - + - - - - - - - - - - + + + + + + + + + + + - A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). - IEDB - IEDB - dissociation constant KD|binding assay|nM - assay measuring the dissociation constant [KD] of a MHC:ligand complex + cytometric bead array assay measuring epitope specific interleukin-3 production by T cells + + A cytometric bead array assay that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-3 production by T cells - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + + + + + + + + + + - A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. - IEDB - IEDB - dissociation constant KD|purified MHC/direct/radioactivity|nM - radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-3 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells - + - + - - - - - + + + + + + + + + + + - A MHC binding constant determination assay measuring half life of binding. - IEDB - IEDB - half life|binding assay|min - assay measuring the half life of a MHC:ligand complex + assay measuring epitope specific granzyme A release by T cells + + A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. + IEDB + IEDB + granzyme A release|biological activity + assay measuring epitope specific granzyme A release by T cells - + - + - - - - - - - - - - - - - - + + + + + + + + + + + - A MHC binding constant determination assay measuring half maximal effective concentration (EC50). - IEDB - IEDB - half maximal effective concentration (EC50)|binding assay|nM - assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex + assay measuring epitope specific granulysin release by T cells + + A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. + IEDB + IEDB + granulysin release|biological activity + assay measuring epitope specific granulysin release by T cells - + - + - - - - - + - + + + + + + + + + + + - A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). - IEDB - IEDB - half maximal inhibitory concentration (IC50)|binding assay|nM - assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex + cytometric bead array assay measuring epitope specific interleukin-27 production by T cells + + A cytometric bead array assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-27 production by T cells - + - + - - - - - + - - - - - - - - - - + + + + + + + + + + + - A MHC binding constant determination assay measuring binding off rate measurement data item (koff). - IEDB - IEDB - off rate|binding assay|1/s - assay measuring the off rate measurement [koff] of a MHC:ligand complex + intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells + + A flow cytometry assay that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells - + - + - - - - - + - + + + + + + + + + + + - A MHC binding constant determination assay measuring binding on rate (kon). - IEDB - IEDB - on rate|binding assay|nM^-1s^-1 - assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex + ELISPOT assay measuring epitope specific interleukin-27 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-27 production by T cells - + - + - - - - - + - + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-27 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-27 release|ELISA + ELISA measuring epitope specific interleukin-27 production by T cells + + + + + + + + + + + - - + + + + + + + + + + + + - An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|chromatography|1/nM - chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells - + - + - + - - + + + + + + epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + + A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific chemokine (C-X-C motif) ligand 13 production by T cells + + + + + + + + + + + - + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-18 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-18 production by T cells + + + + + + + + + + + - - - - - - - + + - An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|chromatography|nM - chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + epitope specific chemokine (C-X-C motif) ligand 12 production by T cells + + A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific chemokine (C-X-C motif) ligand 12 production by T cells - + - + - + - - + + + + + + + epitope specific chemokine (C-C motif) ligand 22 production by T cells + + A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific chemokine (C-C motif) ligand 22 production by T cells + + + + + + + + + + + + + + + + + + epitope specific chemokine (C-X-C motif) ligand 16 production by T cells + + A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific chemokine (C-X-C motif) ligand 16 production by T cells + + + + + + + + + + + - + + + + + + + + + + + - A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - qualitative binding|hydrogen/deuterium exchange footprinting assay - hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex + ELISPOT assay measuring epitope specific interleukin-22 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-22 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-22 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-22 production by T cells - + - + - - - - - + - + + + + + + + + + + + - A immunohistochemistry assay that detects the binding of an antigen with an antibody. - IEDB - IEDB - qualitative binding|immunohistochemistry - immunohistochemistry assay measuring binding of a B cell epitope:antibody complex + ELISPOT assay measuring epitope specific interleukin-23 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-23 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-23 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-23 production by T cells - + - + - + - - + + + + + + epitope specific chemokine (C-C motif) ligand 21 production by T cells + + A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific chemokine (C-C motif) ligand 21 production by T cells + + + + + + + + + + + - + + + + + + + + + + + - A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex. - IEDB - IEDB - 3D structure|any method - 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex + intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells + + A flow cytometry assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells - + - - - Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 - - An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Illumina GA IIx - Illumina Genome Analyzer IIx - ENCODE group - Genome Analyzer IIx + + + + + + + + + + + + + epitope specific chemokine (C-C motif) ligand 19 production by T cells + + A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt + epitope specific chemokine (C-C motif) ligand 19 production by T cells - + - - - - - - - - - Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-21 production by T cells - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng - HiSeq 2000 - http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf - Illumina HiSeq 2000 + An enzyme-linked immunospot assay that detects interleukin-21 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-21 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-21 production by T cells - + - - - - - - - - - Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - HiSeq 2500 - http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf - Illumina HiSeq 2500 + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - + - - - - - - - - - Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina MiSeq - http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf - MiSeq + A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|cytometric bead array + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - + - - - Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Illumina Infinium Human Methylation 450K BeadChip - http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn - Methylation 450K BeadChip + An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + CCL1/TCA-3 release|ELISPOT + ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells - + - - - Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-17F production by T cells - A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Illumina Infinium Human Methylation 27K BeadChip - http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf - Methylation 27K BeadChip + An enzyme-linked immunospot assay that detects interleukin-17F production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17F release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-17F production by T cells - + - - - Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-17F production by T cells - A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Illumina Human 1M-Duo Infinium HD BeadChip - http://www.illumina.com/technology/infinium_hd_assay.ilmn - 1M-Duo Infinium HD BeadChip + An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17F release|ELISA + ELISA measuring epitope specific interleukin-17F production by T cells - + - - - - - - - - - Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells - A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Applied Biosystems SOLiD 3 Plus System - http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf - SOLiD 3 Plus System + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17F release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells - + - - - - - - - - - Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-17A production by T cells - A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Nimblegen Mouse 385K Whole Genome CGH Tiling Array - http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf - Mouse 385K Whole Genome CGH Tiling Array + An enzyme-linked immunospot assay that detects interleukin-17A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17A release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-17A production by T cells - + - - + + + + + + + + - - + + - Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 + drawing a conclusion + Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. +Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. + + + A planned process in which new information is inferred from existing information. + drawing a conclusion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific interleukin-18 production by T cells - A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array - http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf - Mouse 3x720K Whole Genome CGH Tiling Array + A cytometric bead array assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-18 production by T cells - + - - - - - - - - - Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells - A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Nimblegen Human 3x720K Whole Genome CGH Tiling Array - http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf - Human 3x720K Whole Genome CGH Tiling Array + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells - + - - - - - - - - - Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interleukin-16 production by T cells - A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 - http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf - Human 2.1M Whole-Genome CGH Tiling Array v2.0 + An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|ELISA + ELISA measuring epitope specific interleukin-16 production by T cells - + - - - - - - - - - Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-16 production by T cells - A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg - Pacific Biosciences RS II - http://www.pacificbiosciences.com/products/ - PacBio RS II + An enzyme-linked immunospot assay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-16 production by T cells - + - - - - - - - - - Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells - A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed "V2" per https://github.com/obi-ontology/obi/issues/831 on 20180511. - https://www.nanostring.com/products/mirna-assays/mirna-panels - nCounter Human miRNA Expression array + A flow cytometry assay that detects interleukin-16 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-16 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17A release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells + + A flow cytometry assay that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells + + An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells. + IEDB + IEDB + IL-1b release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-12 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-12 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells + + A flow cytometry assay that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-15 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-15 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-15 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-15 production by T cells + + + + + + + + @@ -54116,7 +59526,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54124,7 +59534,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54140,12 +59550,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - + @@ -54156,10 +59561,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - + @@ -54183,7 +59585,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54192,23 +59594,66 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. - Chris Stoeckert - Jie Zheng - DNA methylation ChIP-chip - Penn group - DNA methylation profiling by ChIP-chip assay - - + + + + + + + + + + + + + + + + + + + + + + + + chromatin interaction analysis by paired-end tag sequencing assay + Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] + + An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. + Chris Stoeckert + Jie Zheng + Venkat Malladi + ChIA-PET + ChIA-PET assay + url:http://en.wikipedia.org/wiki/ChIA-PET + chromatin interaction analysis by paired-end tag sequencing assay + + - + - + + + structural analysis by paired-end tag sequencing assay + Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] + + An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. + Chris Stoeckert + Jie Zheng + Venkat Malladi + DNA-PET + DNA-PET assay + PMID:23029419 + structural analysis by paired-end tag sequencing assay + + + + + + + @@ -54221,7 +59666,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54229,7 +59674,41 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -54237,7 +59716,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54246,27 +59725,83 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). - Chris Stoeckert - Jie Zheng - expression MPSS - url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing - transcription profiling by MPSS assay + + + + + + + + + + + + + transcript analysis by paired-end tag sequencing assay + Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] + + A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology. + Chris Stoeckert + Jie Zheng + Venkat Malladi + RNA-PET + RNA-PET assay + PMID:22113299 + transcript analysis by paired-end tag sequencing assay - + - - + + + transcription start site identification objective + + A transcription profiling identification objective that aims to characterize the transcription start sites of genes. + Person: Chris Stoeckert, Jie Zheng + Penn Group + transcription start site identification objective + + + + + + + + + + + + + + + + + + + paired-end library preparation + + A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. + Person: Venkat Malladi, Jie Zheng + Venkat Malladi, Jie Zheng + ENCODE project + paired-end library preparation + + + + + + + + @@ -54278,7 +59813,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54286,7 +59821,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54302,12 +59837,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - + @@ -54318,10 +59848,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - + @@ -54336,7 +59863,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + @@ -54345,7 +59878,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54355,40 +59888,47 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - + - + - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. - Chris Stoeckert - Jie Zheng - histone modification ChIP-chip - Penn group - histone modification identification by ChIP-chip assay + DNase I hypersensitive sites sequencing assay + Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] + + An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. + Chris Stoeckert + Jie Zheng + Venkat Malladi + url:http://en.wikipedia.org/wiki/DNase-Seq + DNase I hypersensitive sites sequencing assay - + - - + + + protein and RNA interaction identification objective + + A sequence feature identification objective that aims to characterize the interactions between protein and RNA. + JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. + Person: Jie Zheng + Jie Zheng + protein and RNA interaction identification objective + + + + + + + + @@ -54421,15 +59961,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - - - - - - + + @@ -54437,13 +59972,34 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + - - + + + + + + + + + + + + @@ -54458,7 +60014,19 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + + + + @@ -54467,7 +60035,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54480,37 +60048,31 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - + - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. - Chris Stoeckert - Jie Zheng - histone modification ChIP-Seq - Penn group - histone modification identification by ChIP-Seq assay + RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay + Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] + + An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). + Chris Stoeckert + Jie Zheng + Venkat Malladi + RIP-seq + RIP-seq assay + PMID:21172659 + RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay - + - - + + @@ -54522,7 +60084,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54530,7 +60092,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54546,12 +60108,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - + @@ -54562,10 +60119,104 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cross-linking immunoprecipitation high-throughput sequencing assay + Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] + + An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. + Chris Stoeckert + Jie Zheng + Venkat Malladi + CLIP-seq + CLIP-seq assay + HITS-CLIP + PMID:18978773 + cross-linking immunoprecipitation high-throughput sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -54580,7 +60231,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + @@ -54589,7 +60246,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54599,7 +60256,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54608,7 +60265,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54619,20 +60276,25 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - A transcription factor binding site assay that utilizes ChIP-chip technology. - Chris Stoeckert - Jie Zheng - TF Binding ChIP-chip - Penn group - transcription factor binding site identification by ChIP-chip assay + formaldehyde-assisted isolation of regulatory elements assay + Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] + + An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. + Chris Stoeckert + Jie Zheng + Venkat Malladi + FAIRE-seq + FAIRE-seq assay + url:http://en.wikipedia.org/wiki/FAIRE-Seq + formaldehyde-assisted isolation of regulatory elements assay - + - - + + @@ -54668,12 +60330,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - + @@ -54684,10 +60341,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - + @@ -54702,7 +60356,13 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + @@ -54711,7 +60371,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54730,7 +60390,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -54738,195 +60398,111 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - A transcription factor binding site assay that utilizes ChIP-seq technology. - Chris Stoeckert - Jie Zheng - TF Binding ChIP-Seq - Penn group - transcription factor binding site identification by ChIP-Seq assay - - - - - - - - - - - - - - - - - - - An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. - Chris Stoeckert - Jie Zheng - Penn group - epigenetic modification assay + methylation-sensitive restriction enzyme sequencing assay + Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] + + An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. + Chris Stoeckert + Jie Zheng + Venkat Malladi + MRE-seq + MRE-seq assay + PMID:20613842 + methylation-sensitive restriction enzyme sequencing assay - + - - + + - - + + - A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina NextSeq 500 - http://systems.illumina.com/systems/nextseq-sequencer.html - NextSeq 500 - - - - - - - - - - + + - A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - HiSeq 1000 - http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf - Illumina HiSeq 1000 + reduced representation bisulfite sequencing assay + Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174] + + A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. + Chris Stoeckert + Jie Zheng + Venkat Malladi + RRBS + RRBS assay + reduced representation bisulfite-seq + PMC:1258174 + reduced representation bisulfite sequencing assay - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Affymetrix HT Human Genome U133 Plus 2 Array Plate Set - HG-U133 Plus 2 - HG-U133 Plus 2 array - http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 - Human Genome U133 Plus 2.0 tiling array + shotgun bisulfite-seq assay + Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. + + A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Shotgun bisulfite sequencing + WGBS + WGSBS + whole genome bisulfite sequencing + whole-genome shotgun bisulfite sequencing + PMID:18278030 + shotgun bisulfite-seq assay - + - - - - - - - - - An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Applied Biosystems SOLiD 4 System - SOLiD 4 - http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 - SOLiD 4 System - - - - - - - - - - - - - - - A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Affymetrix Human Exon 1.0 St Array - Human Exon 1.0 - Human Exon 1.0 ST Array - http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 - Human Exon 1.0 ST tilling array - - - - - - - - - - - - - - - A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Affymetrix HT Human Genome U133 Array Plate Set - HG-U133 - HG-U133 array - http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 - Human Genome U133 tiling array - - - - - - - - - An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. - Person: Venkat Malladi, Chris Stoeckert, Jie Zheng - Illumina GA IIe - Illumina Genome Analyzer IIe - http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf - Genome Analyzer IIe - - - - - - - - - - A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. - - Related tracker:https://sourceforge.net/p/obi/obi-terms/720/ - Person:Chris Stoeckert - PMID:15905473 - SAGE ditag library preparation - - - - - - - + @@ -54952,127 +60528,6 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - - - - - - - PMID:15905473 - - A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced. - Chris Stoeckert - Janos Demeter - Jie Zheng - SAGE - PMID:7570003 - https://sourceforge.net/p/obi/obi-terms/720/ - serial analysis of gene expression assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID:19521816 - - A genotyping by array assay that uses tiling array technology. - Chris Stoeckert - Janos Demeter - Jie Zheng - DNA sequence variation detection by tiling array - PMID:19521816 - https://sourceforge.net/p/obi/obi-terms/720/ - genotyping by tiling array assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - PMID:20080586 - - A genotyping by array assay that uses SNP array technology. - Chris Stoeckert - Janos Demeter - Jie Zheng - DNA sequence variation detection by snp array - PMID:20393561 - https://sourceforge.net/p/obi/obi-terms/720/ - genotyping by SNP array assay - - - - - - - - @@ -55108,1135 +60563,1164 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - pmid:20811459 - A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes - Chris Stoeckert - Janos Demeter - PARS - PMID:20811459 - https://sourceforge.net/p/obi/obi-terms/725/ - parallel analysis of RNA structure assay - - - - - - - - - pmid:23580730 - An RNA-seq assay that combines TL-seq with polysome fractionation - Chris Stoeckert - Janos Demeter - TATL-seq - PMID:23580730 - https://sourceforge.net/p/obi/obi-terms/725/ - translation-associated transcript leader sequencing assay - - - - - - - - - pmid:23580730 - An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. - Chris Stoeckert - Janos Demeter - TL-seq - PMID:23580730 - https://sourceforge.net/p/obi/obi-terms/725/ - transcript leader sequencing assay - - - - - - - - - A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. - Chris Stoeckert - Janos Demeter - PMF - protein fingerprinting - ERO:0001668 - url:http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting - https://sourceforge.net/p/obi/obi-terms/725/ - peptide mass fingerprinting assay - - - - - - - - - pmid:23580730 - An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. - Chris Stoeckert - Janos Demeter - OBI:0000870 - https://sourceforge.net/p/obi/obi-terms/725/ - array based nucleic acid structure mapping assay - - - - - - - - - pmid:17873876 - An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays - Chris Stoeckert - Janos Demeter - https://sourceforge.net/p/obi/obi-terms/725/ - micrococcal nuclease digestion followed by tiling array assay - - - - - - - - - Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 - A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Ribo-seq - Ribo-seq assay - ribosomal profiling - PMID:24468696 - ribosomal profiling by sequencing assay - - - - - - - - - Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. - An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. - Chris Stoeckert - Jie Zheng - Venkat Malladi - ATAC-seq - ATAC-seq assay - PMID:24097267 - assay for transposase-accessible chromatin using sequencing - - - - - - - - - + - Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111. - A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. - Chris Stoeckert - Jie Zheng - Venkat Malladi - ChIRP-seq - ChIRP-seq assay - Chromatin Isolation by RNA purification - PMID:21963238 - chromatin isolation by RNA purification sequencing assay - - - - - - - - - Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. - An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. - Chris Stoeckert - Jie Zheng - Venkat Malladi - STARR-seq - STARR-seq assay - self-transcribing active regulatory region sequencing - PMID:23328393 - self-transcribing active regulatory region sequencing assay - - - - - - - - - Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. - A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. - Chris Stoeckert - Jie Zheng - Venkat Malladi - Carbon-copy chromosome conformation capture assay followed by sequencing - HiC - HiC assay - PMID:19815776 - carbon-copy chromosome conformation capture assay followed by sequencing assay - - - - - - - - - Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 - A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. - Chris Stoeckert - Jie Zheng - Venkat Malladi - iCLIP - iCLIP assay - individual-nucleotide resolution cross-linking and immunoprecipitation - doi:10.1016/j.ymeth.2013.10.011 - individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay - - - - - - - - - An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). - Chris Stoeckert - Jie Zheng - Venkat Malladi - RBNS - RNA Bind-n-Seq - RNBS assay - doi: 10.1016/j.molcel.2014.04.016 - RNA Bind-n-Seq assay - - - - - - - - - Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. - A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. - Chris Stoeckert - Jie Zheng - Venkat Malladi - PAS-seq - PAS-seq assay - Poly(A)-site sequencing - poly(A)-site sequencing assay - doi: 10.1261/rna.2581711 - polyA-site sequencing assay + + + + + + + + + + + + + RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay + Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] + + An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. + Chris Stoeckert + Jie Zheng + Venkat Malladi + RAMPAGE + PMID:22936248 + RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay - + - + - - - - - - - surface plasmon resonance sensor chip - ProteOn GLC Sensor Chip #176-5011 - - A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached - Anna Maria Masci - SPR sensor chip - biosensor chip - sensor chip - OBI - surface plasmon resonance sensor chip + assay array + + A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. + PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Penn Group + assay array - + - - + + - + - - + + - - + + + + + + + - + - - + + - enzyme-linked antibody - Goat anti-Mouse IgG-HRP (horse radish peroxidase) is an antibody linked to the enzyme horseradish peroxidase (HRP) that catalyzes the conversion of chromogenic substrates into colored products producing light when acting on chemiluminescent substrates (ECL). - - A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. - Bjoern Peters, Randi Vita, James A. Overton - OBI - enzyme-linked antibody + secondary cultured cell + + A cultured cell that has been passaged or derives from a cell that has been passaged in culture. + The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. + Person: Matthew Brush + PERSON: Matthew Brush + A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. + secondary cultured cell - + - - + + - - + + + establishing cell line - A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. - PERSON: Sagar Jain, Richard Scheuermann - HiSeq 3000 - http://www.illumina.com/systems/hiseq-3000-4000.html - Illumina HiSeq 3000 + a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). + 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. + Person: Matthew Brush + PERSON:Matthew Brush + establishing cell line - + - - + + + + + + + + + + + + + + + + genetic material + + A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. + MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. + +Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion). + genomic material + hereditary genetic material + OBI developer calls, March 4 2013 and March 11 2013 + Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material. + +Qualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. + +Non-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells). + + genetic material + + + + + + + + + Illumina BeadChip - A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. - PERSON: Sagar Jain, Richard Scheuermann - HiSeq 4000 - http://www.illumina.com/systems/hiseq-3000-4000.html - Illumina HiSeq 4000 + An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. + PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi + http://www.illumina.com/technology/beadarray_technology.ilmn + Illumina BeadChip - + - + - - - - - + - + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex. - IEDB - IEDB - 3D structure|any method - 3D molecular structure determination assay of a MHC:ligand complex + Illumina methylation BeadChip + + A BeadChip made for an analyte assay that generates information about DNA methylation. + PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Penn Group + Illumina methylation BeadChip - + - - - - - - - - - - - - - - - + + - - - - - - - - - - - - + + - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden. - IEDB - IEDB - pathogen burden after challenge|in vivo assay - in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden + LSRFortessa X-20 + + A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. + Anna Maria Masci + http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg + LSRFortessa X-20 - + - - + + - + - - - - - - - + + + + + - + + + + + + + + + + + + + + + + + + + - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden. - IEDB - IEDB - tumor burden after challenge|in vivo assay - in vivo assay measuring B cell epitope specific protection from tumor challenge + sequence assembly process + + A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). + PRS/AGB: +changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. + + Alejandra Gonzalez-Beltran + PERSON: Jie Zheng, Chris Stoeckert + Philippe Rocca-Serra + NIAID GSCID-BRC metadata working group + NIAID GSCID-BRC + sequence assembly process - + - - - - - - - - - - - - + + + + + + + + + + + + + + + number of errors + Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. +PMID: 23587118. see table2 + + a data item that is the number of times that a given process failed, as an integer + Alejandra Gonzalez-Beltran + Philippe Rocca-Serra + PRS, AGB + number of errors + + + + + + + + + + + + + + + - - + + - - - - - - A microarray assay that detects the binding of an antigen with an antibody. - IEDB - IEDB - qualitative binding|microarray - microarray assay measuring binding of a B cell epitope:antibody complex + + + + + + random access memory size + Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. +PMID: 23587118. +"However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads" + + random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation + Alejandra Gonzalez-Beltran + Philippe Rocca-Serra + PRS, AGB + random access memory size - + - + + + cultured immune cell population + + a cultured cell population comprised of a single type of immune system cell + MHB 3-5-13: created as a (temporary) organizational class to organize IEDB immune cultured cell population types. These were all previously labled as 'cell cultures' - and relabeld here as 'cultured cell populations' since a CLO alignment outcome was to use the term 'cell culture' to refer to cultured cells + media. Consult with BP as to whether this organizational class is useful and if so, how to define it. Also check whether the intent was to represent cell populations rather than cell cultures. + PERSON:Matthew Brush + immune cell culture sample + PERSON:Matthew Brush + cultured immune cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell culture + + A material entity comprised of cultured cells and the media in which they are being propagated or stored. + PERSON:Matthew Brush + OBI-CLO Alignment Working Group (Spring 2013) + A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored. + cell culture + + + + + + + + + random access memory + + Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location + Alejandra Gonzalez-Beltran + Philippe Rocca-Serra + RAM + http://en.wikipedia.org/wiki/RAM +last accessed: 2013-12-02 + random access memory + + + + + + + + + + + + + + + establishing primary cell culture + Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages. +Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488 + +When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium. + + an establishing cell culture process whereby cells explanted directly from an organismal source or specimen, and placed in culture for maintenance or propagation as a primary cell culture + PERSON: Matthew Brush + Cells are originally plated at a certain concentration referred to as seeding density. Upon a first passage this primary culture becomes a secondary cell culture that can be propagated to become a stable and homogneous cell line. This class covers establishment of primary cultures from any native cell - 'in vivo' cells isolated from some multicellular organism, or 'in environment' unicellular organisms isolated from some natural environment. + establishing primary cell culture + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - + + - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. - IEDB - IEDB - dissociation constant KD|nuclear magnetic resonance (NMR)|nM - NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + + + + + + + reagent + + A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. + 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. + PERSON:Matthew Brush + PERSON:Matthew Brush + (copied from ReO) +Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. + +Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. + +In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). + reagent - + - + - + - - - - - - - - - - - - + + - A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the recongition of the epitope. - IEDB - IEDB - biological activity|any method - assay measuring biological activity resulting from T cell epitope:MHC:TCR binding + organization of specimen provider principal investigator + + An organization that is the affiliation of the principal investigator providing the specimens for the investigation + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sample Provider PI's Institution + NIAID GSCID-BRC + organization of specimen provider principal investigator - + - + - + - - - - - - - - - - - - - - - - - + + - A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells. - IEDB - IEDB - CCL17/TARC release|biological activity - assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells + organization of Bioinformatics Resource Center contact person + + An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Bioinformatics Resource Center Contact's Institution + NIAID GSCID-BRC + organization of Bioinformatics Resource Center contact person - + - - - - - - - - + + + + + + + + + + + + + + + - + - + - - + + - - - - - - A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells. - IEDB - IEDB - MIF release|biological activity - assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells + + + + + + target material in specimen specification + Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome. + + A plan specification which specifies the type of material that will be assayed in an investigation. + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Target Material + NIAID GSCID-BRC + target material in specimen specification - + - + - + - - - - - - - - - - - - - - - - - + + + + + + - A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells. - IEDB - IEDB - oncostatin M release|biological activity - assay measuring epitope specific oncostatin M production by T cells + Bioinformatics Resource Center contact person + + A person who is the contact representative of a Bioinformatics Resource Center + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Bioinformatics Resource Center Contact Name + NIAID GSCID-BRC + Bioinformatics Resource Center contact person - + - + + + + + + + + + + + + + + + + + + + + specimen-based scope of investigation specification + Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic. + + A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sample Scope + NIAID GSCID-BRC + specimen-based scope of investigation specification + + + + + + + - - - - - + - + - - - - + + + + + + + + + + + + + + + + + + + - A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. - IEDB - IEDB - binding constant|binding assay - assay measuring a binding constant of a T cell epitope:MHC:TCR complex + specimen repository organization + + An organization that provides a service to store and distribute specimens + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Specimen Repository + NIAID GSCID-BRC + specimen repository organization - + - + - + - - - - - - - - - - - - - - - - - + + - A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells. - IEDB - IEDB - CCL17/TARC release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells + email address of Bioinformatics Resource Center contact person + + An email address of the person who is contact representative of a Bioinformatics Resource Center + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Bioinformatics Resource Center Contact's email + NIAID GSCID-BRC + email address of Bioinformatics Resource Center contact person - + - + - + - - - - - - - - - - - - - - - - - + + + + + + - A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells. - IEDB - IEDB - CCL22/MDC release|cytometric bead array - cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + sequencing facility contact person + + A person who is the contact representative at the sequencing facility + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sequencing Facility Contact Name + NIAID GSCID-BRC + sequencing facility contact person - + - + - + - - - - - - - - - + + + + + + - A T cell epitope specific killing assay that uses an in vitro cell killing assay. - IEDB - IEDB - cytotoxicity|in vitro assay - in vitro assay measuring epitope specific T cell killing + specimen provider principal investigator + + A person who is a principal investigator and provides the specimen + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sample Provider Principal Investigator (PI) Name + NIAID GSCID-BRC + specimen provider principal investigator - + - + - + - - - - - - - - - - - - - - - - - + + - A cytometric bead array assay that detects epitope specific granzyme A release by T cells. - IEDB - IEDB - granzyme A release|cytometric bead array - cytometric bead array assay measuring epitope specific granzyme A release by T cells + email address of specimen collector + + An email address of the person collecting the specimen + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Specimen Collector's email + NIAID GSCID-BRC + email address of specimen collector - + - + - + - + - - - - - - - - - - - - - - + + + + + + + + + - A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells. - IEDB - IEDB - granzyme A release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells + sequencing facility organization + + An organization that provides sequence determination service + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sequencing Facility + NIAID GSCID-BRC + sequencing facility organization - + - - - - - - - - + + + + + + + + + + + + + + + - + - - - - - - - + + + + - + + + + + + specification of data to be generated in an investigation + Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype + + An objective specification which indicates the type of data that will be generated and submitted to a database. + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Project Objectives + NIAID GSCID-BRC + specification of data to be generated in an investigation + + + + + + + + + + + + + + - A cytometric bead array assay that detects epitope specific granzyme B release by T cells. - IEDB - IEDB - granzyme B release|cytometric bead array - cytometric bead array assay measuring epitope specific granzyme B release by T cells + organization of specimen collector + + An organization that is the affiliation of the person collecting the specimen + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Specimen Collector's Institution + NIAID GSCID-BRC + organization of specimen collector - + - + - + - - - - - - - - - - - - - - - - - + + - A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells - IEDB - IEDB - granzyme B release|RNA/DNA detection - detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells + email address of sequencing facility contact person + + An email address of the contact representative at the sequencing facility + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sequencing Facility Contact's email + NIAID GSCID-BRC + email address of sequencing facility contact person - + - + - + - - - - - - - - - - - - - - - - - + + - A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells. - IEDB - IEDB - MIF release|cytometric bead array - cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells + specimen collector + + A person who collects the specimen + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Specimen Collector Name + NIAID GSCID-BRC + specimen collector - + - + + + + + + + + + + + + + + + investigation assay specification + Some examples of Project Method are Sequence, Array, Mass Spectrometry + + A plan specification which indicates the assay type used to obtain data. + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Project Method + NIAID GSCID-BRC + investigation assay specification + + + + + + + - + - - - - - - - - - - - - - - - - - + + - A cytometric bead array assay that detects oncostatin M production by T cells. - IEDB - IEDB - oncostatin M release|cytometric bead array - cytometric bead array assay measuring epitope specific oncostatin M production by T cells + organization of sequencing facility contact person + + An organization that is the affiliation of the contact representative at the sequencing facility + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sequencing Facility Contact's Institution + NIAID GSCID-BRC + organization of sequencing facility contact person - + - + - + - + + + + + + + + + + + + + + + + + + + + comment on investigation + + A textual entity that is about any of the aspects of an investigation worth noting + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Comments + NIAID GSCID-BRC + comment on investigation + + + + + + + + + + + + + + + + + + + + + - + + + + + - + - - + + - - - - - - An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells. - IEDB - IEDB - perforin release|ELISPOT - ELISPOT assay measuring epitope specific perforin release by T cells + + + + + + target capture specification + Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey + + A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Target Capture + NIAID GSCID-BRC + target capture specification - + - + - + - + - - + + + + + @@ -56244,74 +61728,85 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - A T cell epitope specific proliferation assay that is performed in vivo. - IEDB - IEDB - proliferation|in vivo assay - in vivo assay measuring epitope specific proliferation of T cells - - - - - - - - - A T cell epitope specific proliferation assay that is performed on cells in vitro. - IEDB - IEDB - proliferation|in vitro assay - in vitro assay measuring epitope specific proliferation of T cells + specimen identifier assigned by specimen repository + + A specimen identifier which is assigned by a specimen repository + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Specimen Repository Sample ID + NIAID GSCID-BRC + specimen identifier assigned by specimen repository - + - + - - - - - + - + - - - - + + + + + + + + + - An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output. - IEDB - IEDB - qualitative binding|binding assay - assay measuring qualitative binding of a MHC:ligand complex + specimen identifier assigned by sequencing facility + + A specimen identifier which is assigned by a sequencing facility + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sample ID - Sequencing Facility + NIAID GSCID-BRC + specimen identifier assigned by sequencing facility - + - + - + - + - - + + + + + + + + + + + + + + + + + + + @@ -56319,1002 +61814,889 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. - IEDB - IEDB - protection from challenge|in vivo assay - in vivo assay measuring T cell epitope specific protection from challenge - - - - - - - - - T cell epitope dependent biological activity assay that detects suppression of an in vitro response. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - suppression|in vitro assay - in vitro assay measuring T cell epitope specific suppression + sample preparation for sequencing assay + + A sample preparation for assay that preparation of nucleic acids for a sequencing assay + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Nucleic Acid Preparation Method + NIAID GSCID-BRC + sample preparation for sequencing assay - + - + - + - - - - - - - - - - - - - - + + - An immune epitope assay that characterizes the structrue of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule. - IEDB - IEDB - MHC ligand assay|any method - MHC ligand assay + email address of specimen provider principal investigator + + An email address of the principal investigator providing the specimens for the investigation + PERSON: Chris Stoeckert, Jie Zheng + NIAID GSCID-BRC metadata working group + Sample Provider PI's email + NIAID GSCID-BRC + email address of specimen provider principal investigator - + - + - + - - + + - - collection of specimens - Blood cells collected from multiple donors over the course of a study. - - A material entity that has two or more specimens as its parts. - Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ - Person: Chris Stoeckert, Jie Zheng - OBIB, OBI - Biobank - collection of specimens + sequencing service + + A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. + Person: Jie Zheng + Adpated from 'DNA sequencing service' + NIAID GSCID-BRC + sequencing service - + - - - specimens derived from shared ancestor - Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy. - - A collection of specimens derived from one common specimen via one or more material processing process(es). - Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ - Chris Stoeckert, Jie Zheng - specimen family - Duke Biobank, OBIB, OBI - Biobank - specimens derived from shared ancestor + + + + + + + + + + + + + + + + + + + + + secondary cultured cell population + + A cultured cell population that is derived through one or more passages in culture. + The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. + PERSON:Matthew Brush + secondary cell culture sample + PERSON:Matthew Brush + The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. + secondary cultured cell population - + - - - specimen set collection process - Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy. - - A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. - Chris Stoeckert, Jie Zheng - OBIB, OBI - specimen set collection process + + + + + + + + + cancer cell line + + An immortal cell line derived from a transformed cell that was part of a malignant tumor. + cancer cell line - + - - - specimens collected in one encounter - Both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy. - - A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. - Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ - Person: Chris Stoeckert, Jie Zheng - specimen set - OBIB, OBI - Biobank - specimens collected in one encounter + + + + + + + + + immortalizing cell line transformation + + a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture + immortalizing cell line transformation - + - - - - - - - - - - - - - - - - - - - human specimen set + + + testable hypothesis + that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time. - Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ - Person: Chris Stoeckert, Jie Zheng - Duke Biobank, OBIB, OBI - Biobank - human specimen set + An information content entity that expresses an assertion that is intended to be tested. + In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. + + Group:2013 Philly Workshop group + hypothesis + Group:2013 Philly Workshop group + testable hypothesis - + - - - - A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity. - Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ - Person: Chris Stoeckert - Bjoern Peters, OBI - specimens collected longitudinally + + + + + + + + + + + + + + + conclusion based on data + The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. +The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". + + An information content entity that is inferred from data. + In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. + Group:2013 Philly Workshop group + Group:2013 Philly Workshop group + conclusion based on data - + - - - - An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. - Chris Stoeckert - Paul D. Thomas - reporter gene detection assay - Paul D. Thomas, Yang Chai; FaceBase - https://github.com/obi-ontology/obi/issues/781 - reporter gene assay + + + + + + + + + primary cell culture + + A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. + PERSON:Matthew Brush + OBI-CLO Alignment Working Group (Spring 2013) + primary cell culture - + - - - PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules" - - A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. - Paul D. Thomas - Yang Chai - enhancer reporter gene assay - FaceBase - PMID 24614317 - https://github.com/obi-ontology/obi/issues/781 - enhancer activity detection by reporter gene assay + + + + + + + + + cell line culture + + A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored. + PERSON:Matthew Brush + OBI-CLO Alignment Working Group (Spring 2013) + A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored. + cell line culture - + - - - PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue" - A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. - Paul D. Thomas - Yang Chai - chromatin modifier binding site identification by ChIP-Seq assay - PMID:19212405 - https://github.com/obi-ontology/obi/issues/782 - transcription cofactor activity region identification by ChIP-Seq assay + + + cell freezing medium + + A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. + PERSON: Matthew Brush + cell freezing medium - - - - - PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells" - - An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. - Paul D. Thomas - Yang Chai - transcript expression location detection by fluorescent HCR. - PMID:21037591 - https://github.com/obi-ontology/obi/issues/783 - transcript expression location detection by hybridization chain reaction assay - - - + - + + + + + + + + + computation run time + Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. +PMID: 23587118. - - - - A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected. - Bjoern Peters - Chris Stoeckert - Jason Hilton - OBI - TAB-seq - Tet-assisted bisulfite sequencing - PMID:23196972 - http://sourceforge.net/p/obi/obi-terms/789/ - Tet-assisted bisulfite sequencing assay +See Table 4 + + computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency. + + Alejandra Gonzalez-Beltran + Philippe Rocca-Serra + computation run time datum + PRS,AGB + computation run time - + - - - containing a specimen function - - A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay. - For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ - Chris Stoeckert - Duke Biobank, OBIB - Biobank - containing a specimen function + + + + + + + + + multiplex ligation-mediated amplification + + A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. + Chris Stoeckert, Jie Zheng + LMA + MLPA + Multiplex ligation-dependent probe amplification + web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification +Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ + multiplex ligation-mediated amplification - + - - + + + - - - + + + + + + + + + + + + - - - - specimen container - COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube - - A container with the function of containing a specimen. - For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ - Chris Stoeckert - Duke Biobank, OBIB - specimen container - - - - - - - - - - - - - + + - - physical store - a freezer. a humidity controlled box. - - A container with an environmental control function. - For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ - Chris Stoeckert - Duke Biobank, OBIB - physical store - - - - - - - - - rapid amplification of cDNA ends - - A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA. - For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ - Jason Hilton, Chris Stoeckert - RACE - http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/RACE_Rapid_Amplification_of_cDNA_Ends/5_Prime_RACE_and_3_Prime_RACE - ENCODE - rapid amplification of cDNA ends - - - - - - - - - 5' rapid amplification of cDNA ends - - A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 5' end of the mRNA. - For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ - Jason Hilton, Chris Stoeckert - 5' RACE - https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/5-race-system-for-rapid-amplification-of-cdna-ends.html - ENCODE - 5' rapid amplification of cDNA ends - - - - - - - - - 3' rapid amplification of cDNA ends - - A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 3' end of the mRNA. - For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ - Jason Hilton, Chris Stoeckert - 3' RACE - https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/3-race-system-for-rapid-amplification-of-cdna-ends.html - ENCODE - 3' rapid amplification of cDNA ends - - - - - - - - - 5' RNA ligase mediated rapid amplification of cDNA ends - - A 5' rapid amplification pf cDNA ends that uses RNA ligase to add an RNA adapter oligonucleotide to intact 5' mRNA ends, allowing the amplification of cDNA only from full-length, capped mRNA. - For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ - Jason Hilton, Chris Stoeckert - 5' RLM RACE - https://tools.thermofisher.com/content/sfs/manuals/cms_056070.pdf - ENCODE - 5' RNA ligase mediated rapid amplification of cDNA ends - - - - - - - - - MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants. - - A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. - Chris Stoeckert - David Bujold - Capture Methylome - MCC-Seq - MethylC-Capture Sequencing - PMID:26021296 - MethylC-Capture sequencing assay - - - - - - - + - - - + + + + + + + + + + + + - - + + - specimen family creation - Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum. - - A material processing that has as its input a specimen and as its output a collection of specimens. - For details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ - Mathias Brochhausen, Chris Stoeckert, Jie Zheng - OBI, OBIB - Biobank - specimen family creation - - - - - - - - + - - + - - + + + + + - - - - A T cell epitope specific proliferation assay performed on cells in vitro that uses a CFSE assay. - IEDB - IEDB - proliferation|CFSE - carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - + + + + + + + + + - - A T cell epitope binding constant determination assay that measures the dissociation constant KD. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - dissociation constant KD|binding assay|nM - assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DNA replication timing by array assay + Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] + + An assay which quantifies the timing of DNA replication as a function of genome position using array technology. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Repli-chip + Repli-chip assay + PMID:18842067 + DNA replication timing by array assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope binding constant determination assay that measures the on rate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - on rate|binding assay|M^-1s^-1 - assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex + + + DNA replication identification objective + + A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. + Chris Stoeckert, Jie Zheng + Group: Penn Group + DNA replication identification objective - + - - + + + chromosome conformation identification objective + + A molecular feature identification objective that aims to determine spatial organization of chromatin. + Chris Stoeckert, Jie Zheng + Group: Penn Group + chromosome conformation identification objective + + + + + + + + + - - - - - - + - - - - + + + + + + + + + - - - - - - - + + - - A T cell epitope binding constant determination assay that measures the off rate. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - off rate|binding assay|1/s - assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex - - - - - - - - + + - - - - - - + - - - - + + + + + + + + + - + - - - - + + + + + + + + + - - A T cell epitope binding constant determination assay that measures the association constant KA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - association constant KA|binding assay|1/nM - assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + + + + + + + + + + + + + + RNA-binding protein immunoprecipitation array profiling assay + Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] + + An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). + Chris Stoeckert + Jie Zheng + Venkat Malladi + RIP-chip + RIP-chip assay + PMID:21125495 + RNA-binding protein immunoprecipitation array profiling assay - + - - + + + - - - - - - + - - - - + + + + + + + + + + + + + - - A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - 3D structure|small-angle scattering assay - small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex - - - - - - - - + + - - - - - - + - - - - + + + + + + + + + - + - - - - + + + + + + + + + - - A bio-layer interferometry assay that measures the on rate of an antigen with an antibody. - IEDB - IEDB - on rate|bio-layer interferometry assay|M^-1s^-1 - bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Carbon-copy chromosome conformation capture assay + van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] + + An assay that measures the organization of chromosomes at the genome-wide scale. + Chris Stoeckert + Jie Zheng + Venkat Malladi + 5C + 5C assay + PMID:16954542 + Carbon-copy chromosome conformation capture assay - + - - + + + - - - - - - + - - - - + + + + + + + + + - - - - - - - + + - - A bio-layer interferometry assay that measures the off rate of an antigen with an antibody. - IEDB - IEDB - off rate|bio-layer interferometry assay|1/s - bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex - - - - - - - - + + - - - - - - + - - - - + + + + + + + + + + + + + - - A bio-layer interferometry assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|bio-layer interferometry assay - bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex - - - - - - - - + + - - - - - - + - - - - + + + + + + + + + - + - - - - + + + + + + + + + - - A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody. - IEDB - IEDB - dissociation constant KD|bio-layer interferometry assay|nM - bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - - - - - - - - + + + + + + + - + - Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division. - a assay detecting a molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection. - IEDB - CFSE assay - IEDB - carboxyfluorescein succinimidyl ester staining assay - - - - - - - - - Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds. - A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. - IEDB - biolayer interferometry, BLI - IEDB - bio-layer interferometry assay - - - - - - - - - Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein - A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. - IEDB - SAXS - IEDB - small-angle scattering 3D molecular structure determination assay - - - - - - - - - - + + - - A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. - Term request: https://sourceforge.net/p/obi/obi-terms/791/ - Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group - NimbleGen Human 6x630K CGH Whole Genome Tiling Array - http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 - Human 6x630K CGH Whole Genome Tiling Array - - - - - - - - - The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 + + + + + + + + + + + + + + + + + + + + + + + + DNA replication timing by sequencing assay + Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139_�_144. [PMID:19966280] - A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. - Discussed on Aug 22, 2016 OBI dev call. Details see tracker: -https://sourceforge.net/p/obi/obi-terms/818/ - OBI developers - DOI - https://en.wikipedia.org/wiki/Digital_object_identifier -https://www.doi.org/ - digital object identifier - - - - - - - - - - An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. - Chris Stoeckert - Jason Hilton - eCLIP - PMID:27018577 - enhanced cross-linking immunoprecipitation high-throughput sequencing assay - - - - - - - - - - An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. - Chris Stoeckert - Jason Hilton - Mark A. Miller - short RNA-seq - small RNA-seq - url:http://science.sciencemag.org/content/316/5830/1484.full - url:http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html - https://github.com/obi-ontology/obi/issues/859 - small RNA sequencing assay - - - - - - - - - - An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. - Chris Stoeckert - Jason Hilton - Bru-seq - PMC:4009065 - bromouridine labeling and sequencing assay + An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Repli-seq + Repli-seq assay + PMID:19966280 + DNA replication timing by sequencing assay - + - - - - An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. - Chris Stoeckert - Jason Hilton - BruChase-seq - PMC:4009065 - bromouridine pulse-chase and sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + RNA-binding protein immunoprecipitation tiling array profiling assay + Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] + + An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). + Chris Stoeckert + Jie Zheng + Venkat Malladi + PMID:21125495 + RNA-binding protein immunoprecipitation tiling array profiling assay - + - - + + @@ -57323,10 +62705,10 @@ https://www.doi.org/ - + - + @@ -57334,152 +62716,102 @@ https://www.doi.org/ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining refelctive of the level of expression of those surface receptors. - A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. - ImmPort - CyTOF - mass cytometry assay - PMID:26190063 - cytometry time of flight assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. - An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. - ImmPort - HPLC - PMID:9491555 - high performance liquid chromotography assay - - - - - - - - - WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS. - A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. - Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. - ImmPort - WGS - PMID:23095910 - PMID:25827230 - whole genome sequencing assay - - - - - - - - - DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified. - A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). - ImmPort - WES - PMID:25827230 - exome sequencing assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy. - An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. - ImmPort - PMID:21685355 - microscopy assay + + + + + + + + + + + + + + + + + + microRNA profiling by high throughput sequencing assay + Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767 + + A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. + Chris Stoeckert + Jie Zheng + Venkat Malladi + miRNA-HTS + miRNA-seq + microRNA-seq + microRNA-seq assay + url:http://www.ebi.ac.uk/efo/EFO_0002896 + microRNA profiling by high throughput sequencing assay - + - - + + @@ -57488,10 +62820,10 @@ https://www.doi.org/ - + - + @@ -57499,1702 +62831,1473 @@ https://www.doi.org/ - + - T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells. - A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators). - ImmPort - MLR - PMID:14969764 - mixed lymphocyte reaction assay - - - - - - - - - DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself. - A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. - Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. - ImmPort - KIR typing - PMID:21239231 - killer cell immunoglobulin-like receptor typing assay - - - - - - - - - Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both_ according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size_ were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. - A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. - Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. - IEDB - MHC typing, HLA typing - PMC:2628004 - PMID:27516207 - major histocompatibility typing assay - - - - - - - - + + + + + + + + + + + + + + - + + + + + + + + + + + - IHC slide staining - - A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues. - Chris Stoeckert, Ned Haubein - http://www.agilent.com/cs/library/technicaloverviews/public/08002_ihc_staining_methods.pdf - IHC slide staining + + + + + + + + + + + + + protein sequencing by tandem mass spectrometry assay + Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] + + A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. + Chris Stoeckert + Jie Zheng + Venkat Malladi + PMID:3462691 + protein sequencing by tandem mass spectrometry assay - + - + + - + + + + + + + + + + + + + + - + - H&E slide staining - - A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink. - Chris Stoeckert, Ned Haubein - http://www.histalim.com/accueil/activities/our-services/histology/hematoxylin-eosin-2/ - H&E slide staining - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - H&E-stained fixed tissue slide specimen - - A fixed tissue slide specimen that is the output of H&E slide staining. - Chris Stoeckert, Ned Haubein - OBIB, OBI - H&E-stained fixed tissue slide specimen + + + + + + + + + + + + + + + + + + + + + + + + + micrococcal nuclease digestion followed by high throughput sequencing assay + Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] + + An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease + Chris Stoeckert + Jie Zheng + Venkat Malladi + MNase-seq + MNase-seq assay + PMID:17038564 + micrococcal nuclease digestion followed by high throughput sequencing assay - + - + + - - - + + + + + + + + + + + + + + + + - IHC-stained fixed tissue slide specimen - - A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. - Chris Stoeckert, Ned Haubein - immunohistochemistry slide specimen - OBIB, OBI - IHC-stained fixed tissue slide specimen + + + + + + + + + + + + + + + + + + + chromatin immunoprecipitation with exonuclease sequencing assay + Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] + + A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site + Bjoern Peters + Chris Stoeckert + Jie Zheng + Venkat Malladi + ChIP-exo assay + PMID:22153082 + chromatin immunoprecipitation with exonuclease sequencing assay - + - - - - A cell specimen that contains only one cell. - Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ - PERSON: Jie Zheng, Alexander Diehl - PERSON: Jie Zheng, Alexander Diehl - single cell specimen - - - - - - - - - Illumina Genome Analyzer - - A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. - Person: Chris Stoeckert, Jason Hilton - Illumina Genome Analyzer I - http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html - Illumina Genome Analyzer + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + microRNA profiling assay + + A transcription profiling assay that quantifies the microRNA species within a biological sample. + Chris Stoeckert + Jie Zheng + Venkat Malladi + miRNA expression assay + microRNA expression assay + PMID: 23382819 + microRNA profiling assay - + - - - Illumina HiSeq X Ten - - A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. - Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann - HiSeq X Ten - http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html - Illumina HiSeq X Ten + + + + + + + + + + + + + + selection + PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. + + A planned process which results in the creation of group of entity from a larger group by the application of predefined criteria. + this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) + Person: Philippe Rocca-Serra + selection process + OBI + selection - + - - - Illumina Infinium Omni5Exome-4 Kit - - An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. - Person: Chris Stoeckert, Jason Hilton - http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html - Illumina Infinium Omni5Exome-4 Kit + + + + + + + + + + + + + + + mass value specification + + A value specification that specifies the mass of some thing. + PERSON:Bjoern Peters + mass value specification - + - - - Illumina Infinium MethylationEPIC BeadChip - - An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. - Person: Chris Stoeckert, Jason Hilton - http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf - Illumina Infinium MethylationEPIC BeadChip + + + categorical value specification + + A value specification that is specifies one category out of a fixed number of nominal categories + PERSON:Bjoern Peters + categorical value specification - + - - - An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability. - Rob Nash - dynamic SILAC - pulse SILAC - pulsed SILAC - PMID:18954100 - PMID:19053139 - pulse stable isotope labeling by amino acids in cell culture + + + + + + 1 + + + + + + 1 + + + scalar value specification + + A value specification that consists of two parts: a numeral and a unit label + PERSON:Bjoern Peters + scalar value specification - + - - - - - - - - + + + + + + + + + - + - + - - + + + + + + + + + + + + + + + + - - - - - - A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - CCL20/MIP-3a release|cytometric bead array - cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells + + + + + + + + + + + + comparing prediction to measurement + + A planned process in which predicted values for some thing are compared to measured values for that thing. + comparing prediction to measurement - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - CCL20/MIP-3a release|biological activity - assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells + + + value specification + The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. + + An information content entity that specifies a value within a classification scheme or on a quantitative scale. + This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. + PERSON:Bjoern Peters + value specification - + - - + + - + + + + + + + - + - - + + + + + + + - RNA Integrity Number calculation - - A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. - Chris Stoeckert, Bjoern Peters - RIN calculation - https://www.agilent.com/cs/library/applications/5989-1165EN.pdf - RNA Integrity Number calculation - - - - - - - - - RNA Integrity Number value specification - - A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). - Chris Stoeckert, Bjoern Peters - RIN value specification - OBI - RNA Integrity Number value specification + predicted value + + an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. + PERSON:Bjoern Peters + predicted value - + - - - + + + - - - - - - + + - - temperature value specification - - A value specification that specifies the temperature of some thing. - Chris Stoeckert - OBI - temperature value specification + + + predicted mass value + + A predicted value where the prediction specifies the mass of some thing. + PERSON:Bjoern Peters + predicted mass value - + - - - + + + - - + + - - + + + + molecular-labeled material + + a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay + PERSON:Matthew Brush + OBI developer call, 3-12-12 + molecular-labeled material + + + + + + + + + + + + + - volume value specification + + + + + + + genome coverage + Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. +PMID: 23587118. + +"The genome coverage increased from 81.16% to 93.91%" - A value specification that specifies the volume of some thing. - Chris Stoeckert - OBI - volume value specification + A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%. + Alejandra Gonzalez-Beltran + Philippe Rocca-Serra + A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. +Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. +PMID: 22510764 + genome coverage - + - - + + - - - - - - - - - - - - + + - - An assay to determine the temperature of an evaluant. - Bjoern Peters - Chris Stoeckert - OBI - temperature measurement assay + + + + + + + + + + + + + N50 + Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. +PMID: 23587118. + +"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" + + the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly + Alejandra Gonzalez-Beltran + Philippe Rocca-Serra + weighted median item size + adapted from: +"http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" +(from table 7) +and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html" + N50 - + - - + + - + - + - - + + - - An assay to determine the volume of an evaluant. - Bjoern Peters - Chris Stoeckert - OBI - volume measurement assay - - - - - - - - - - A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. - Chris Stoeckert - Jason Hilton - microRNA counts - PMID:26729350 - url:http://www.nanostring.com/applications/technology - https://github.com/obi-ontology/obi/issues/806 - ENCODE DCC - Nanostring nCounter miRNA expression assay - - - - - + contig N50 + Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. +PMID: 23587118. - - - - An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. - Chris Stoeckert - Jason Hilton - BruUV-seq - PMC:4675984 - https://github.com/obi-ontology/obi/issues/827 - ENCODE DCC - bromouride labeling and sequencing after UV exposure +"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" + + N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. + Alejandra Gonzalez-Beltran + Philippe Rocca-Serra + adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html + contig N50 - + - - - - An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. - Chris Stoeckert - Jason Hilton - circulome-seq - eccDNA-seq - url:http://biorxiv.org/content/early/2017/04/19/128686 - https://github.com/obi-ontology/obi/issues/830 - ENCODE DCC - extrachromosomal circular DNA sequencing assay + + + grant agency + + An organization that provides funding support for projects such as investigations. + PERSON: Jie Zheng, Chris Stoeckert + funding organization + NIAID GSCID-BRC metadata working group + NIAID GSCID-BRC + grant agency + 'funding organization' +http://vivoweb.org/ontology/core#FundingOrganization - + - - - Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens - An analyte assay that measures the presence or amount of antibodies to a specified antigen. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - antigen specific antibodies assay + + + software pipeline + + A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. + PERSON: Jie Zheng, Chris Stoeckert + WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29 + NIAID GSCID-BRC + software pipeline - + - - + + - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + + + + + + + + + + + + + - An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. - HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36) - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HIV I/II Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - HIV antibody assay + sequence annotation + + A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. + PERSON: Jie Zheng, Chris Stoeckert + NIAID GSCID-BRC metadata working group + NIAID GSCID-BRC + sequence annotation - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + - An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. - https://www.cdc.gov/mmwr/preview/mmwrhtml/00042810.htm - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HIV I/II Plus O assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - HIV group O antibody assay + scaffold N50 + Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. +PMID: 23587118. + +"Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" + + N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information + Alejandra Gonzalez-Beltran + Philippe Rocca-Serra + adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html + scaffold N50 - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HBsAb assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - surface HBV antibody assay + forward PCR primer + SP6 promoter, forward primer (SP6 TTTAGGTGACACTATAG) + + A short oligonucleotide complementary to target DNA (5'->3' on plus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. + Philippe Rocca-Serra + 5' primer + forward primer + sense primer + adapted from http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p + forward PCR primer - + - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HBcAb assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - core HBV antibody assay + + + sequence annotation provider + + A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. + PERSON: Jie Zheng, Chris Stoeckert + NIAID GSCID-BRC metadata working group + annotation provider + NIAID GSCID-BRC + sequence annotation provider - + - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HBcAb-IgM assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - core HBV IgM antibody assay + + sequence assembly name + + A textual entity that is used to denote a sequence assembly. + PERSON: Jie Zheng, Chris Stoeckert + NIAID GSCID-BRC metadata working group + assembly name + NIAID GSCID-BRC + sequence assembly name - + - - + + + sequence annotation reporting role + + A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. + PERSON: Jie Zheng, Chris Stoeckert + NIAID GSCID-BRC metadata working group + NIAID GSCID-BRC + sequence annotation reporting role + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HCV Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - HCV antibody assay + reverse PCR primer + + 5' end of luciferase, reverse primer (LucNrev CCTTATGCAGTTGCTCTCC) + + A short oligonucleotide complementary to target DNA (5'->3' on minus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. + Philippe Rocca-Serra + 3' primer + antisense primer + reverse primer + adapted from "http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p" + reverse PCR primer - + - - - + + + flash freezing + + A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. + Person: Mathias Brochhausen, Jie Zheng + WEB: http://en.wikipedia.org/wiki/Flash_freezing + flash freezing + + + + + + + + + freezing + + A planned process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities. + Person: Mathias Brochhausen, Jie Zheng + Mathias Brochhausen + freezing + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + - - + + - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - + + + + - - An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - EBV IgG Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - EBV IgG antibody assay + + ChIP assay + PMID: 6379641 + + An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed + Bjoern Peters + Philippe Rocca-Serra + chromatin immunoprecipitation assay + url:https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation + ChIP assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - EBV IgM Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - EBV IgM antibody assay + + + competitive binding reference ligand role + The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion. + + A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. + Bjoern Peters, Randi Vita, James A. Overton + Bjoern Peters + competitive binding reference ligand role - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - CMV Ab assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - CMV antibody assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + - An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - VDRL test - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - venereal disease research laboratory test + assay using chromatin immunoprecipitation + http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html + + An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation + Philippe Rocca-Serra + http://sourceforge.net/p/obi/obi-terms/707/ + assay using chromatin immunoprecipitation - + - - - + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - RPR assay - url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/ - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - rapid plasma reagin test + hardware testing design + + A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. + Person: Jie Zheng + MO_734 hardware_variation_design + hardware testing design - + - - - - - - - - - - - - - - - - - - - - - - - - - - - An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HBsAg assay - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - HBV surface antigen assay + + + systematic review study design + Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ + The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ + + A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. + PERSON: Bill Hogan + systematic review study design - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HIV-1 NAT - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - HIV-1 nucleic acid testing + multiplexed nucleotide library sequencing + http://www.illumina.com/technology/multiplexing_sequencing_assay.ilmn + + A planned process which consists in running a set of samples as a pool on a sequencing instrument, while retaining the ability to associate individual results to each of the individual input samples through the use of a ligated oligonucleotide (the "multiplex identifier sequence"). This oligonucleotide is introduced during the sequence library preparation, and is unique to and specific for all library fragments derived from each sample in a sample pool. + Dan Berrios + PERSON:Philippe Rocca-Serra + OBI + multiplexed nucleotide library sequencing - + - - - + + + - + - - - - - - - - - - - - - - - - - - - + + + + - - - - - - - - - - - - + + - - An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. - Bjoern Peters - Chris Stoeckert - James Overton - Randi Vita - HCV NAT - OBI - https://github.com/obi-ontology/obi/issues/825 - NCI BBRB - HCV nucleic acid testing - - - - - - - - + + taxonomic diversity assessment by targeted gene survey + PMID:20679230 + PMID:25367129 - A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. - Chris Stoeckert - Jason Hilton - Mint-ChIP - Mint-ChIP-seq - url:http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00863-1 - https://github.com/obi-ontology/obi/issues/829 - ENCODE DCC - multiplexed indexed T7 ChIP-seq assay + An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. + Philippe Rocca-Serra + environmental gene survey + targeted gene survey + targeted gene survey DNA barcoding + OBI + taxonomic diversity assessment by targeted gene survey - + - - - A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ - Rebecca Jackson - SELEX - PMID:21720957 - systematic evolution of ligands by exponential enrichment assay + + + PCR program + https://www.neb.com/protocols/1/01/01/taq-dna-polymerase-with-standard-taq-buffer-m0273 + + a PCR program is a plan specification which is executed during a polymerase chain reaction (PCR) by a thermocycler instrument that will iterate through the changes in temperature and duration of each of the annealing, denaturation, elongation steps for as many times as specified by the program. + PERSON:Philippe Rocca-Serra + OBI + PCR program - - - - - An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. - Bjoern Peters - doi:10.1002/3527600906.mcb.200300025 - footprinting assay - - - + - + + + target gene specification + http://www.ncbi.nlm.nih.gov/pubmed/25367129 - - - An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis - Rebecca Jackson - OBI development call - DNAse footprinting assay +"performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene) + + is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey + PERSON:Philippe Rocca-Serra + PRS for OBI + target gene + target gene specification - - - - - A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. - Rebecca Jackson - ECO:0001095 - PMID:9043710 - mammalian 2-hybrid assay - - - + - + + + target subfragment specification + http://www.ncbi.nlm.nih.gov/pubmed/23335919 - - - An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. - Rebecca Jackson - OBI development call - protein localization assay +"performing a profiling of microbial phylogenetic composition using massively-parallel pyrotag sequencing targeting the V9 hypervariable region (used as target subfragment) of the 18S ribosomal RNA (rRNA) gene (used as target gene) + + is a directive information specifying a genomic region, possibly located in a coding genomic region, which is the focus of a planned process such as an assay, for instance in a environmental gene survey + PERSON:Philippe Rocca-Serra + PRS for OBI + target subfragment + target subfragment specification - + - - - A protein localization assay that determines the specific location of a protein in a living tissue sample. - Rebecca Jackson - PMID:14686950 - tissue-based protein localization assay + + + decision-theoretic analysis objective + + An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. + The best action to take is typically defined as the one that maximizes expected utility. + PERSON: Bill Hogan + decision analysis objective + PERSON: Bill Hogan + decision-theoretic analysis objective - + - - - + + + - - - - - - - - - - - - - - - - + + - - A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. - Rebecca Jackson - ECO - subcellular protein localization assay + + decision analysis study design + + a study design that has a decision analysis objective specification as part + PERSON: Bill Hogan + PERSON: Bill Hogan + decision analysis study design - + - - - An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. - Rebecca Jackson - ECO - subcellular protein immunohistochemistry assay + + + + + + + + + sequence library data demultiplexing + + is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to separate all reads belonging to a given single sample following the sequencing of a multiplexed library + PERSON: Philippe Rocca-Serra + PRS for OBI + sequence library data demultiplexing - + - - + + - + - - + + - A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. - Chris Stoeckert - PMID:18388953 - ChIP-qPCR assay + multiplexing sequence identifier + We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. in http://www.ncbi.nlm.nih.gov/pubmed/22574170 + + A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library + PERSON:Philippe Rocca-Serra + OBI + multiplexing sequence identifier - + - - - A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. - Chris Stoeckert - PMID:20541015 - genomic SELEX + + + + + + + + + + + + + + + operational taxonomic unit matrix + http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1610290/ + + Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism. + + PERSON:Philippe Rocca-Serra + PRS for OBI + operational taxonomic unit matrix - + - - - An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. - Bjoern Peters - dot blot analysis - PMID:10473518 - dot blot assay + + + biodiversity assessment objective + + biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level + PERSON:Philippe Rocca-Serra + PRS for OBI + biodiversity assessment objective - + - - - A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. - Bjoern Peters - Northwestern analysis - Northwestern assay - PMID:26965261 - Northwestern blot assay + + + + + + + + + + + + + + + + + + + + + + multiplexed sequencing library + http://www.ncbi.nlm.nih.gov/pubmed/24997861 + +Nat Methods. 2014 Aug;11(8):834-40. doi: 10.1038/nmeth.3022. Epub 2014 Jul 6. +Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run. + PERSON:Philippe Rocca-Serra + DNA-barcoded sequencing library + PRS for OBI + multiplexed sequencing library - + - - - A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. - Bjoern Peters - PMID:26404144 - Southwestern blot assay + + + Ion 316 Chip v2 + + An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. + Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ + PERSON: Sagar Jain + Ion 316 Chip + Ion PGM 316 Chip + Ion PGM 316 Chip v2 + http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html + Ion 316 Chip v2 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed - Bjoern Peters - immunocytochemistry + + + Ion 318 Chip v2 + + An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. + Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ + PERSON: Sagar Jain + Ion 318 Chip + Ion PGM 318 Chip + Ion PGM 318 Chip v2 + http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html + Ion 318 Chip v2 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. - Rebecca Jackson - ATP quantitation assay - cell viability ATP quantitation assay - ECO - ATP bioluminescence assay + + + ion semiconductor chip + + An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface. + Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/ + PERSON: Sagar Jain + ion chip + ion integrated circuit + ion semiconductor + http://www.thefreedictionary.com/Semiconductor+chip + ion semiconductor chip - + - - - An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance). - Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues. - Gully Burns - url:https://en.wikipedia.org/wiki/Electrophysiology - electrophysiology assay + + + Ion 314 Chip v2 + + An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb. + Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/ + PERSON: Sagar Jain + Ion 314 Chip + Ion PGM 314 Chip + Ion PGM 314 Chip v2 + http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html + Ion 314 Chip v2 - + - - + + @@ -59203,10 +64306,10 @@ https://www.doi.org/ - + - + @@ -59214,62 +64317,79 @@ https://www.doi.org/ - + - An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations. - Gully Burns - ECO:0006012 - url:http://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.46.030184.002323 - url:https://en.wikipedia.org/wiki/Patch_clamp - patch clamp assay + hydrogen/deuterium exchange footprinting assay + Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface. + + A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. + IEDB + IEDB + hydrogen/deuterium exchange footprinting assay - + - - - + + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. - Gully Burns - ECO:0006015 - url:https://en.wikipedia.org/wiki/Patch_clamp#Whole-cell_recording_or_whole-cell_patch - whole-cell patch clamp assay + + cytometry assay + An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. + + An assay that counts and/or measures characteristics of cells. + IEDB + IEDB + cytometry assay - + - - + + @@ -59281,7 +64401,7 @@ https://www.doi.org/ - + @@ -59289,23 +64409,11 @@ https://www.doi.org/ - + - A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. - Gully Burns - url:https://en.wikipedia.org/wiki/Patch_clamp#Cell-attached_patch - cell-attached patch clamp assay - - - - - - - - @@ -59314,10 +64422,10 @@ https://www.doi.org/ - + - + @@ -59325,61 +64433,58 @@ https://www.doi.org/ - + - A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations. - Gully Burns - url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ - url:https://en.wikipedia.org/wiki/Patch_clamp#Inside-out_patch - inside-out patch clamp assay + + + + + + + immunoblot assay + + An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. + IEDB + IEDB + immunoblot assay - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + - A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels. - Gully Burns - url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ - url:https://en.wikipedia.org/wiki/Patch_clamp#Outside-out_patch - outside-out patch clamp assay + fluorescence quenching binding assay + + A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. + IEDB + IEDB + fluorescence quenching binding assay - + - - + + @@ -59388,10 +64493,10 @@ https://www.doi.org/ - + - - + + @@ -59399,260 +64504,317 @@ https://www.doi.org/ - - - - - - An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. - Gully Burns - url:https://en.wikipedia.org/wiki/Voltage_clamp - voltage clamp assay - - - - - - - - - - - - - - + - - + + - - - - - The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation. - Gully Burns - TEVC - url:https://en.wikipedia.org/wiki/Voltage_clamp#Two-electrode_voltage_clamp_using_microelectrodes - two electrode voltage clamp assay + in vivo intervention experiment + Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival. + + An assay in which the effect of a targeted process (the intervention) on an organism is tested. + The intervention in an experiment should be modeled accordingly to the intevention carried out in a human cllinical trial, which is currently modeled as 'study intervention'. This touches the boundaries of study vs. assay. + IEDB + IEDB + in vivo intervention experiment - + - - - - - - - - - - - - - - - - - - - - - - - - - - - The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques. - Gully Burns - COVG - PMID:9711615 - cut open oocyte voltage clamp assay + + + disease exacerbation in vivo intervention experiment + Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide. + + An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. + Should have data about disease severity as readout; could just use disease for now + IEDB + IEDB + disease exacerbation in vivo intervention experiment - + - - - The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels. - Gully Burns - url:https://en.wikipedia.org/wiki/Electrophysiology#Current_clamp - current clamp assay + + + protection from challenge in vivo intervention experiment + Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide. + + An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. + should have challenge as intervention + IEDB + IEDB + protection from challenge in vivo intervention experiment - + - - - An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. - Gully Burns - EEG - electroencephalography + + + tolerance induction intervention experiment + Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide. + + An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. + should have tolerance induction as intervention + IEDB + IEDB + tolerance induction intervention experiment - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique. - Can be used on any cell, not just neurons. - Gully Burns - url:http://www.thieme.com/media/samples/pubid-80418214.pdf - single-unit recording + + + treatment intervention experiment + Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals. + + An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. + should have treatment as intervention + IEDB + IEDB + treatment intervention experiment - + - - - An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. - Gully Burns - multi-unit recording + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + microarray assay + Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray. + + An analyte assay where binding of the analyte to immobilized matrix is measured. + IEDB + IEDB + microarray assay - + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + immunohistochemistry + Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. + + An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. + IEDB + IEDB + immunohistochemistry + + + + + + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - + + assay measuring the association constant [KA] of a MHC:ligand complex + + A MHC binding constant determination assay measuring equilibrium association constant (KA). + IEDB + IEDB + association constant KA|binding assay|1/M + assay measuring the association constant [KA] of a MHC:ligand complex + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring the dissociation constant [KD] of a MHC:ligand complex + + A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). + IEDB + IEDB + dissociation constant KD|binding assay|nM + assay measuring the dissociation constant [KD] of a MHC:ligand complex + + + + + + + + + + + + + - + - - - - - - - - - - - - + + @@ -59663,1931 +64825,2980 @@ https://www.doi.org/ - - - - - - - - - + - - + + - - - - - - - - - + + - - - - An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. - Gully Burns - doi:10.1007/978-1-4614-7320-6_723-1 - local field potential recording - - - - - - - - - - - - - - - + + + - - + + - - - - - - courier organization - - An organization that delivers messages, packages, and mail. - Chris Stoeckert, Helena Ellis - courier - https://en.wikipedia.org/wiki/Courier - NCI BBRB - courier organization + + + + + + + + + + + + + + + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex + + A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. + IEDB + IEDB + dissociation constant KD|purified MHC/direct/radioactivity|nM + radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex - + - - - courier tracking number - - A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - courier tracking number + + + + + + + + + + + + + + + + + + + + + + assay measuring the half life of a MHC:ligand complex + + A MHC binding constant determination assay measuring half life of binding. + IEDB + IEDB + half life|binding assay|min + assay measuring the half life of a MHC:ligand complex - + - - - Leica Peloris rapid tissue processor - - An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. - Chris Stoeckert, Helena Ellis - http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf - NCI BBRB - Leica Peloris rapid tissue processor + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex + + A MHC binding constant determination assay measuring half maximal effective concentration (EC50). + IEDB + IEDB + half maximal effective concentration (EC50)|binding assay|nM + assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex - + - - - Microm Ergostar HM200 - - A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right. - Chris Stoeckert, Helena Ellis - http://www.ultra-medical.com/Microm-Ergostar-HM200-Microtome/en - NCI BBRB - Microm Ergostar HM200 + + + + + + + + + + + + + + + + + + + + + + assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex + + A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). + IEDB + IEDB + half maximal inhibitory concentration (IC50)|binding assay|nM + assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex - + - - - microtome blade - - A device that is the part of a microtome used to slice specimens to a desired thickness. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Microtome - NCI BBRB - microtome blade + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring the off rate measurement [koff] of a MHC:ligand complex + + A MHC binding constant determination assay measuring binding off rate measurement data item (koff). + IEDB + IEDB + off rate|binding assay|1/s + assay measuring the off rate measurement [koff] of a MHC:ligand complex - + - - - Sakura Low profile Accu-Edge microtome blade - - A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering. - Chris Stoeckert, Helena Ellis - http://www.sakura.eu/Our-products/item/8/Microtomy/29/Accu-Edge-Disposable-Microtome-Blades - NCI BBRB - Sakura Low profile Accu-Edge microtome blade + + + + + + + + + + + + + + + + + + + + + + assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex + + A MHC binding constant determination assay measuring binding on rate (kon). + IEDB + IEDB + on rate|binding assay|nM^-1s^-1 + assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex - + - - - tissue section thickness - - A length measurement datum that is the result of an assay measuring the thickness of a tissue section. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - tissue section thickness + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex + + An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|chromatography|1/nM + chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex - + - + - + - + + + + + - - - - - - - - - + + + + + + + + + + + + + - - molecular analysis facility organization - An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs. - - An organization that provides molecular analysis service. - Chris Stoeckert, Helena Ellis - MAF - NCI BBRB, OBIB - NCI BBRB - molecular analysis facility organization + chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|chromatography|nM + chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - - - - - cannot be assessed, not applicable, unknown - An information content entity that provides an explanation why a data item is not provided. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB - reason for lack of data item - - - + - - - - - A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. - Chris Stoeckert, Helena Ellis - cannot be assessed - OBI - NCI BBRB - cannot be assessed determination + + + + + + + + + + + + + + + + + + + + + + hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex + + A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + qualitative binding|hydrogen/deuterium exchange footprinting assay + hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex - + - - - A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB - determination if assay will provide reliable results + + + + + + + + + + + + + + + + + + + + + + immunohistochemistry assay measuring binding of a B cell epitope:antibody complex + + A immunohistochemistry assay that detects the binding of an antigen with an antibody. + IEDB + IEDB + qualitative binding|immunohistochemistry + immunohistochemistry assay measuring binding of a B cell epitope:antibody complex - + - - - AJCC 7th edition GX: cannot be assessed. - A cannot be assessed determination for histologic tumor grade. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB - GX + + + + + + + + + + + + + + + + + + + + + + 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex + + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex. + IEDB + IEDB + 3D structure|any method + 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex - + - - - AJCC 7th edition pTX: cannot be assessed. - A cannot be assessed determination for pathologic primary tumor staging. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB - pTX + + + Genome Analyzer IIx + Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 + + An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Illumina GA IIx + Illumina Genome Analyzer IIx + ENCODE group + Genome Analyzer IIx - + - - - AJCC 7th edition pNX: cannot be assessed. - A cannot be assessed determination of pathologic staging of lymph nodes. - Chris Stoeckert, Helena Ellis - OBI - NCI BBRB - pNX + + + + + + + + + Illumina HiSeq 2000 + Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 + + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng + HiSeq 2000 + http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf + Illumina HiSeq 2000 - + - - - G1:Well differentiated - G4: Undifferentiated - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - histologic grade according to AJCC 7th edition + + + + + + + + + Illumina HiSeq 2500 + Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 + + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + HiSeq 2500 + http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf + Illumina HiSeq 2500 - + - - - A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. - Chris Stoeckert, Helena Ellis - Histologic Grade (Fuhrman Nuclear Grading System) - NCI BBRB, OBI - NCI BBRB - histologic grade according to the Fuhrman Nuclear Grading System + + + + + + + + + MiSeq + Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] + + A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng + Illumina MiSeq + http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf + MiSeq - + - - - A categorical value specification that is a histologic grade assigned to a ovarian tumor. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - histologic grade for ovarian tumor + + + Methylation 450K BeadChip + Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 + + A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Illumina Infinium Human Methylation 450K BeadChip + http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn + Methylation 450K BeadChip - + - - - A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - histologic grade for ovarian tumor according to a two-tier grading system + + + Methylation 27K BeadChip + Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 + + A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Illumina Infinium Human Methylation 27K BeadChip + http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf + Methylation 27K BeadChip - + - - - A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - histologic grade for ovarian tumor according to the World Health Organization + + + 1M-Duo Infinium HD BeadChip + Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 + + A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Illumina Human 1M-Duo Infinium HD BeadChip + http://www.illumina.com/technology/infinium_hd_assay.ilmn + 1M-Duo Infinium HD BeadChip - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic primary tumor stage for colon and rectum according to AJCC 7th edition + + + + + + + + + SOLiD 3 Plus System + Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 + + A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Applied Biosystems SOLiD 3 Plus System + http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf + SOLiD 3 Plus System - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread lung primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic primary tumor stage for lung according to AJCC 7th edition + + + + + + + + + Mouse 385K Whole Genome CGH Tiling Array + Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ + + A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Nimblegen Mouse 385K Whole Genome CGH Tiling Array + http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf + Mouse 385K Whole Genome CGH Tiling Array - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic primary tumor stage for kidney according to AJCC 7th edition + + + + + + + + + Mouse 3x720K Whole Genome CGH Tiling Array + Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 + + A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array + http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf + Mouse 3x720K Whole Genome CGH Tiling Array - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic primary tumor stage for ovary according to AJCC 7th edition + + + + + + + + + Human 3x720K Whole Genome CGH Tiling Array + Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 + + A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Nimblegen Human 3x720K Whole Genome CGH Tiling Array + http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf + Human 3x720K Whole Genome CGH Tiling Array - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic lymph node stage for colon and rectum according to AJCC 7th edition + + + + + + + + + Human 2.1M Whole-Genome CGH Tiling Array v2.0 + Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 + + A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 + http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf + Human 2.1M Whole-Genome CGH Tiling Array v2.0 - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic lymph node stage for lung according to AJCC 7th edition + + + + + + + + + PacBio RS II + Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 + + A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg + Pacific Biosciences RS II + http://www.pacificbiosciences.com/products/ + PacBio RS II - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic lymph node stage for kidney according to AJCC 7th edition + + + + + + + + + nCounter Human miRNA Expression array + Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 + + A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed "V2" per https://github.com/obi-ontology/obi/issues/831 on 20180511. + https://www.nanostring.com/products/mirna-assays/mirna-panels + nCounter Human miRNA Expression array - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. - Chris Stoeckert, Helena Ellis - pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic lymph node stage for ovary according to AJCC 7th edition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DNA methylation profiling by ChIP-chip assay + + An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. + Chris Stoeckert + Jie Zheng + DNA methylation ChIP-chip + Penn group + DNA methylation profiling by ChIP-chip assay - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: colon distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic distant metastases stage for colon according to AJCC 7th edition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transcription profiling by MPSS assay + + A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). + Chris Stoeckert + Jie Zheng + expression MPSS + url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing + transcription profiling by MPSS assay - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: lung distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic distant metastases stage for lung according to AJCC 7th edition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + histone modification identification by ChIP-chip assay + + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. + Chris Stoeckert + Jie Zheng + histone modification ChIP-chip + Penn group + histone modification identification by ChIP-chip assay - + - - - A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: kidney distant Metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic distant metastases stage for kidney according to AJCC 7th edition - - - - - - - - - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. - Chris Stoeckert, Helena Ellis - M: ovarian distant metastases (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - pathologic distant metastases stage for ovary according to AJCC 7th edition - - - - - - - - - A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. - Chris Stoeckert, Helena Ellis - Clinical tumor stage group (AJCC 7th Edition) - NCI BBRB, OBI - NCI BBRB - clinical tumor stage group according to AJCC 7th edition - - - - - - - - - A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. - Chris Stoeckert, Helena Ellis - Clinical FIGO stage - NCI BBRB, OBI - NCI BBRB - International Federation of Gynecology and Obstetrics cervical cancer stage value specification - - - - - - - - - A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. - Chris Stoeckert, Helena Ellis - Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) - NCI BBRB, OBI - NCI BBRB - International Federation of Gynecology and Obstetrics ovarian cancer stage value specification - - - - - - - - - A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). - Chris Stoeckert, Helena Ellis - Performance Status Scale - https://en.wikipedia.org/wiki/Performance_status - NCI BBRB - performance status value specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + histone modification identification by ChIP-Seq assay + + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. + Chris Stoeckert + Jie Zheng + histone modification ChIP-Seq + Penn group + histone modification identification by ChIP-Seq assay - + - - - A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. - Chris Stoeckert, Helena Ellis - ECOG score - NCI BBRB, OBI - NCI BBRB - Eastern Cooperative Oncology Group score value specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transcription factor binding site identification by ChIP-chip assay + + A transcription factor binding site assay that utilizes ChIP-chip technology. + Chris Stoeckert + Jie Zheng + TF Binding ChIP-chip + Penn group + transcription factor binding site identification by ChIP-chip assay - + - - - A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. - Chris Stoeckert, Helena Ellis - Karnofsky Score - NCI BBRB, OBI - NCI BBRB - Karnofsky score vaue specification + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transcription factor binding site identification by ChIP-Seq assay + + A transcription factor binding site assay that utilizes ChIP-seq technology. + Chris Stoeckert + Jie Zheng + TF Binding ChIP-Seq + Penn group + transcription factor binding site identification by ChIP-Seq assay - + - - - A clinical history in which there is a diagnosis of cancer. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - clinical history of cancer + + + + + + + + + + + + + epigenetic modification assay + + An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. + Chris Stoeckert + Jie Zheng + Penn group + epigenetic modification assay - + - - - A clinical history in which there was no diagnosis of cancer. - Chris Stoeckert, Helena Ellis - clinical history of no cancer - NCI BBRB, OBIB - NCI BBRB - clinical history devoid of cancer + + + + + + + + + NextSeq 500 + + A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Illumina NextSeq 500 + http://systems.illumina.com/systems/nextseq-sequencer.html + NextSeq 500 - + - - - A clinical history in which it is not known whether there was a diagnosis of cancer. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - unknown clinical history of cancer + + + + + + + + + Illumina HiSeq 1000 + + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + HiSeq 1000 + http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf + Illumina HiSeq 1000 - + - - - A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer. - Chris Stoeckert, Helena Ellis - cancer diagnosis - OBIB - NCI BBRB - diagnosis of cancer + + + + + + + + + Human Genome U133 Plus 2.0 tiling array + + A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Affymetrix HT Human Genome U133 Plus 2 Array Plate Set + HG-U133 Plus 2 + HG-U133 Plus 2 array + http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 + Human Genome U133 Plus 2.0 tiling array - + - - - A clinical history in which there is a diagnosis of cancer in a blood relative. - Chris Stoeckert, Helena Ellis - family history of cancer - NCI BBRB, OBIB - NCI BBRB - family clinical history of cancer + + + + + + + + + SOLiD 4 System + + An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Applied Biosystems SOLiD 4 System + SOLiD 4 + http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 + SOLiD 4 System - + - - - A clinical history in which there is a diagnosis of cancer in the female sibling of a parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - aunt clinical history of cancer + + + + + + + + + Human Exon 1.0 ST tilling array + + A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Affymetrix Human Exon 1.0 St Array + Human Exon 1.0 + Human Exon 1.0 ST Array + http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 + Human Exon 1.0 ST tilling array - + - - - A clinical history in which there is a diagnosis of cancer in a male sibling. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - brother clinical history of cancer + + + + + + + + + Human Genome U133 tiling array + + A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Affymetrix HT Human Genome U133 Array Plate Set + HG-U133 + HG-U133 array + http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 + Human Genome U133 tiling array - + - - - A clinical history in which there is a diagnosis of cancer in a person's female child. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - daughter clinical history of cancer + + + Genome Analyzer IIe + + An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. + Person: Venkat Malladi, Chris Stoeckert, Jie Zheng + Illumina GA IIe + Illumina Genome Analyzer IIe + http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf + Genome Analyzer IIe - + - - - A clinical history in which there is a diagnosis of cancer in a male parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - father clinical history of cancer + + + SAGE ditag library preparation + + A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. + + Related tracker:https://sourceforge.net/p/obi/obi-terms/720/ + Person:Chris Stoeckert + PMID:15905473 + SAGE ditag library preparation - - - - - A clinical history in which there is a diagnosis of cancer in a female parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - mother clinical history of cancer - - - + - - - - - A clinical history in which there is a diagnosis of cancer in a female sibling. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - sister clinical history of cancer - - - - - - - - - A clinical history in which there is a diagnosis of cancer in a person's male child. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - son clinical history of cancer - - - - - - - - - A clinical history in which there is a diagnosis of cancer in a male sibling of a parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - uncle clinical history of cancer - - - - - - - - - A clinical history in which there is a diagnosis of cancer in a female parent of a parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - grandmother clinical history of cancer - - - - - - - - - A clinical history in which there is a diagnosis of cancer in a male parent of a parent. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - grandfather clinical history of cancer - - - - - - - - - A clinical history in which there is a diagnosis of cancer in a male child of a sibling. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - nephew clinical history of cancer + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + serial analysis of gene expression assay + PMID:15905473 + + A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced. + Chris Stoeckert + Janos Demeter + Jie Zheng + SAGE + PMID:7570003 + https://sourceforge.net/p/obi/obi-terms/720/ + serial analysis of gene expression assay - + - - - A clinical history in which there is a diagnosis of cancer in a female child of a sibling. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - niece clinical history of cancer + + + + + + + + + + + + + + + + + + + + + + + + + + + genotyping by tiling array assay + PMID:19521816 + + A genotyping by array assay that uses tiling array technology. + Chris Stoeckert + Janos Demeter + Jie Zheng + DNA sequence variation detection by tiling array + PMID:19521816 + https://sourceforge.net/p/obi/obi-terms/720/ + genotyping by tiling array assay - + - - - A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - diagnosis of infectious disease + + + + + + + + + + + + + + + + + + + + + + + + + + + genotyping by SNP array assay + PMID:20080586 + + A genotyping by array assay that uses SNP array technology. + Chris Stoeckert + Janos Demeter + Jie Zheng + DNA sequence variation detection by snp array + PMID:20393561 + https://sourceforge.net/p/obi/obi-terms/720/ + genotyping by SNP array assay - + - - - A diagnosis of infectious disease caused by the hepatitis B virus. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - diagnosis of hepatitis B + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + parallel analysis of RNA structure assay + pmid:20811459 + + A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes + Chris Stoeckert + Janos Demeter + PARS + PMID:20811459 + https://sourceforge.net/p/obi/obi-terms/725/ + parallel analysis of RNA structure assay - + - - - A diagnosis of infectious disease caused by the hepatitis C virus. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - diagnosis of hepatitis C + + + translation-associated transcript leader sequencing assay + pmid:23580730 + + An RNA-seq assay that combines TL-seq with polysome fractionation + Chris Stoeckert + Janos Demeter + TATL-seq + PMID:23580730 + https://sourceforge.net/p/obi/obi-terms/725/ + translation-associated transcript leader sequencing assay - + - - - A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - diagnosis of HIV + + + transcript leader sequencing assay + pmid:23580730 + + An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. + Chris Stoeckert + Janos Demeter + TL-seq + PMID:23580730 + https://sourceforge.net/p/obi/obi-terms/725/ + transcript leader sequencing assay - + - - - A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - clinical history of repeated HIV assays + + + peptide mass fingerprinting assay + + A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. + Chris Stoeckert + Janos Demeter + PMF + protein fingerprinting + ERO:0001668 + url:http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting + https://sourceforge.net/p/obi/obi-terms/725/ + peptide mass fingerprinting assay - + - - - A clinical history in which there has been second hand exposure to tobacco smoking. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - exposure to second hand smoke + + + array based nucleic acid structure mapping assay + pmid:23580730 + + An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. + Chris Stoeckert + Janos Demeter + OBI:0000870 + https://sourceforge.net/p/obi/obi-terms/725/ + array based nucleic acid structure mapping assay - + - - - An exposure to second hand smoke that occurred in the (patient's) household when the person was a child. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - exposure to second hand smoke in household during childhood + + + micrococcal nuclease digestion followed by tiling array assay + pmid:17873876 + + An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays + Chris Stoeckert + Janos Demeter + https://sourceforge.net/p/obi/obi-terms/725/ + micrococcal nuclease digestion followed by tiling array assay - + - - - An exposure to second hand smoke in person's current household. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - exposure to second hand smoke in current household + + + ribosomal profiling by sequencing assay + Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 + + A RNA-seq assay that sequences only mRNA protected by the ribosome during translation. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Ribo-seq + Ribo-seq assay + ribosomal profiling + PMID:24468696 + ribosomal profiling by sequencing assay - + - - - A clinical history in which a female has had a pregnancy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - pregnancy history + + + assay for transposase-accessible chromatin using sequencing + Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. + + An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. + Chris Stoeckert + Jie Zheng + Venkat Malladi + ATAC-seq + ATAC-seq assay + PMID:24097267 + assay for transposase-accessible chromatin using sequencing - + - - - A measurement datum of the total number of pregnancies a woman has had. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - number of pregnancies + + + + + + + + + + + + + + + + chromatin isolation by RNA purification sequencing assay + Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111. + + A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. + Chris Stoeckert + Jie Zheng + Venkat Malladi + ChIRP-seq + ChIRP-seq assay + Chromatin Isolation by RNA purification + PMID:21963238 + chromatin isolation by RNA purification sequencing assay - + - - - A measurement datum of the total number of live births a female has had. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - number of live births + + + self-transcribing active regulatory region sequencing assay + Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. + + An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. + Chris Stoeckert + Jie Zheng + Venkat Malladi + STARR-seq + STARR-seq assay + self-transcribing active regulatory region sequencing + PMID:23328393 + self-transcribing active regulatory region sequencing assay - + - - - An age measurement datum performed on a female when her first biological child was born. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - age when gave birth to first child + + + carbon-copy chromosome conformation capture assay followed by sequencing assay + Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. + + A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. + Chris Stoeckert + Jie Zheng + Venkat Malladi + Carbon-copy chromosome conformation capture assay followed by sequencing + HiC + HiC assay + PMID:19815776 + carbon-copy chromosome conformation capture assay followed by sequencing assay - + - - - A clinical history in which a woman has had gynecologic surgery in the past. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - gynecologic surgery history + + + individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay + Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 + + A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. + Chris Stoeckert + Jie Zheng + Venkat Malladi + iCLIP + iCLIP assay + individual-nucleotide resolution cross-linking and immunoprecipitation + doi:10.1016/j.ymeth.2013.10.011 + individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay - + - - - A gynecologic surgery history in which a woman has had a hysterectomy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - hysterectomy history + + + RNA Bind-n-Seq assay + + An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). + Chris Stoeckert + Jie Zheng + Venkat Malladi + RBNS + RNA Bind-n-Seq + RNBS assay + doi: 10.1016/j.molcel.2014.04.016 + RNA Bind-n-Seq assay - + - - - A gynecologic surgery history in which a woman has had a unilateral oophorectomy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - unilateral oophorectomy history + + + polyA-site sequencing assay + Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. + + A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level. + Chris Stoeckert + Jie Zheng + Venkat Malladi + PAS-seq + PAS-seq assay + Poly(A)-site sequencing + poly(A)-site sequencing assay + doi: 10.1261/rna.2581711 + polyA-site sequencing assay - + - - - A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - neither hysterectomy nor oophorectomy history + + + + + + + + + + + + + + + surface plasmon resonance sensor chip + ProteOn GLC Sensor Chip #176-5011 + + A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached + Anna Maria Masci + SPR sensor chip + biosensor chip + sensor chip + OBI + surface plasmon resonance sensor chip - + - - - An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - hormonal birth control use history + + + + + + + + + + + + + + + + + + + + + + + enzyme-linked antibody + Goat anti-Mouse IgG-HRP (horse radish peroxidase) is an antibody linked to the enzyme horseradish peroxidase (HRP) that catalyzes the conversion of chromogenic substrates into colored products producing light when acting on chemiluminescent substrates (ECL). + + A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. + Bjoern Peters, Randi Vita, James A. Overton + OBI + enzyme-linked antibody - + - - - A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - hormonal birth control former use history + + + + + + + + + Illumina HiSeq 3000 + + A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + PERSON: Sagar Jain, Richard Scheuermann + HiSeq 3000 + http://www.illumina.com/systems/hiseq-3000-4000.html + Illumina HiSeq 3000 - + - - - A hormonal birth control use history that indicates an individual is currently a hormonal birth control user. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - hormonal birth control current use history + + + + + + + + + Illumina HiSeq 4000 + + A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + PERSON: Sagar Jain, Richard Scheuermann + HiSeq 4000 + http://www.illumina.com/systems/hiseq-3000-4000.html + Illumina HiSeq 4000 - + - - - A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - no hormonal birth control use history + + + + + + + + + + + + + + + + + + + + + + 3D molecular structure determination assay of a MHC:ligand complex + + A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex. + IEDB + IEDB + 3D structure|any method + 3D molecular structure determination assay of a MHC:ligand complex - + - - - A clinical history in which an individual has had hormonal replacement therapy in the past. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - hormonal replacement therapy history + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden + + An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden. + IEDB + IEDB + pathogen burden after challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden - + - - - A processed material used for delivery of hormones in hormone replacement therapy. - Chris Stoeckert, Helena Ellis - form of hormone replacement therapy - NCI BBRB, OBIB - NCI BBRB - delivery form for hormonal replacement therapy - - - - - - - - - A delivery form for hormonal replacement therapy that is a pill for oral administration. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - pill delivery form for hormonal replacement therapy + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection after tumor burden challenge + + An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden. + IEDB + IEDB + tumor burden after challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection after tumor burden challenge - + - - - A delivery form for hormonal replacement therapy that is a patch for transdermal administration. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - patch delivery form for hormonal replacement therapy + + + + + + + + + + + + + + + + + + + + + + microarray assay measuring binding of a B cell epitope:antibody complex + + A microarray assay that detects the binding of an antigen with an antibody. + IEDB + IEDB + qualitative binding|microarray + microarray assay measuring binding of a B cell epitope:antibody complex - + - - - A delivery form for hormonal replacement therapy that is a cream for transdermal administration. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - cream delivery form for hormonal replacement therapy + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. + IEDB + IEDB + dissociation constant KD|nuclear magnetic resonance (NMR)|nM + NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - + - - - An information content entity that indicates the state of a female's cessation of menstruation. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - menopausal status + + + + + + + + + + + + + + + + + + + + + + + assay measuring biological activity resulting from T cell epitope:MHC:TCR binding + + A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the recongition of the epitope. + IEDB + IEDB + biological activity|any method + assay measuring biological activity resulting from T cell epitope:MHC:TCR binding - + - - - A menopausal status that is neither pre- nor post-menopausal. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - indeterminate menopausal status + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells + + A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells. + IEDB + IEDB + CCL17/TARC release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells - + - - - A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - premenopausal status + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells + + A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells. + IEDB + IEDB + MIF release|biological activity + assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells - + - - - A menopausal status indicating that it has been 6-12 months since last menstrual period. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - perimenopausal status + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific oncostatin M production by T cells + + A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells. + IEDB + IEDB + oncostatin M release|biological activity + assay measuring epitope specific oncostatin M production by T cells - + - - - A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - postmenopausal status + + + + + + + + + + + + + + + + + + + + + + assay measuring a binding constant of a T cell epitope:MHC:TCR complex + + A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. + IEDB + IEDB + binding constant|binding assay + assay measuring a binding constant of a T cell epitope:MHC:TCR complex - + - - - A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - exposure to environmental and workplace carcinogens history + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells. + IEDB + IEDB + CCL17/TARC release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells - + - - - An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - exposure to arsenic history + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells + + A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells. + IEDB + IEDB + CCL22/MDC release|cytometric bead array + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells - + - - - An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - exposure to asbestos history + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro assay measuring epitope specific T cell killing + + An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. + IEDB + IEDB + cytotoxicity|in vitro assay + in vitro assay measuring epitope specific T cell killing - + - - - An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - exposure to diesel exhaust history + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific granzyme A release by T cells + + A cytometric bead array assay that detects epitope specific granzyme A release by T cells. + IEDB + IEDB + granzyme A release|cytometric bead array + cytometric bead array assay measuring epitope specific granzyme A release by T cells - + - - - An exposure to environmental and workplace carcinogens history where the carcinogen is chromium. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - exposure to chromium history + + + + + + + + + + + + + + + + + + + + + + + + + + + + detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells + + A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells. + IEDB + IEDB + granzyme A release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells - + - - - An exposure to environmental and workplace carcinogens history where the carcinogen is silica. - Chris Stoeckert, Helena Ellis - OBIB - NCI BBRB - exposure to silica history + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific granzyme B release by T cells + + A cytometric bead array assay that detects epitope specific granzyme B release by T cells. + IEDB + IEDB + granzyme B release|cytometric bead array + cytometric bead array assay measuring epitope specific granzyme B release by T cells - + - - - An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process. - Chris Stoeckert, Helena Ellis - eligibility criterion met - NCI BBRB, OBIB - NCI BBRB - indicator of whether an inclusion criterion was met - - - - - - - - - An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process. - Chris Stoeckert, Helena Ellis - all eligibility criteria met - NCI BBRB, OBIB - NCI BBRB - indicator of whether all inclusion criteria were met - - - - - - - - - An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - age of majority inclusion criterion - - - - - - - - - An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - chemotherapy treatment exclusion criterion - - - - - - - - - An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - radiation treatment exclusion criteria - - - - - - - - - An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years. - An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - chemotherapy treatment within the recent past exclusion criterion - - - - - - - - - An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years. - An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - radiation treatment within the recent past exclusion criterion - - - - - - - - - An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0 - An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - BMI range inclusion criterion - - - - - - - - - An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death. - An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - blood transfusion exclusion criterion - - - - - - - - - An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - history of metastatic cancer exclusion criterion - - - - - - - - - Donor eligibility based on history of intravenous drug abuse in the last 5 years. - An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - intravenous drug use exclusion criterion - - - - - - - - - Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years. - An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - history of sex with someone with a history of blood borne infection exclusion criterion - - - - - - - - - Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years. - An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - history of sex with someone with a history of intravenous drugs exclusion criterion - - - - - - - - - An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - HIV exclusion criterion - - - - - - - - - Donor eligibility based on whether the donor has been exposed to HIV/AIDS. - An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBIB - NCI BBRB - exposure to blood borne infectious disease exclusion criterion - - - - - - - - - - - - - - - - - - - - - - An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. - Rebecca Jackson - PMID:26463381 - RNA interactome capture - - - - - - - - - A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. - Jie Zheng - WFM - url:http://bitesizebio.com/19409/the-many-flavors-of-widefield-microscopy/ - url:https://svi.nl/WideFieldMicroscope - widefield microscopy assay - - - - - - - - - - - - - - - - - - - - - An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. - Chris S - PMID:8327891 - nuclear ligation assay - - - - - - - - - - - - - - - A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. - Chris S - 3C assay - PMID:11847345 - url:http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.243.html - chromosome conformation capture assay - - - - - - - - - A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. - Chris S - PMID:20461051 - Hi-C assay - - - - - - - - - An assay that produces a description of the qualities of an entity that has not been transformed, through observation and physical, non-invasive techniques. - physical examination of individual - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. - Jie Zheng - PMID:21770468 - hydroxyl-radical footprinting assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. - Jie Zheng - MPE-Fe(II) footprinting - PMID:6225070 - PMID:6435669 - methidiumpropyl-EDTA-iron(II) footprinting assay - - - - - - - - - - - - - - - A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. - Person: Alan Ruttenberg, Jie Zheng - https://en.wiktionary.org/wiki/measurand - https://github.com/obi-ontology/obi/issues/778 - measurand role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. - Rebecca Jackson - PMID:23378648 - url:https://en.wikipedia.org/wiki/Primer_extension - transcription start site mapping by primer extension assay - - - - - - - - - A study design in which proteins in a sample are detected, quantified or otherwise analysed. - Dan Berrios - OBI:0001441 - proteomic profiling design - - - - - - - - - An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library. - Rebecca Jackson - SSH - subtractive hybridization - PMID:14970460 - suppression subtractive hybridization - - - - - - - - - An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. - Rebecca Jackson - DSH - differential screening - PMID:25472628 - differential screening hybridization + + detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells + + A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells + IEDB + IEDB + granzyme B release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells - + - + - - - - - + - + + + + + + + + + + + - A footprinting assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - qualitative binding|footprinting assay - footprinting assay measuring binding of a B cell epitope:antibody complex + cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells + + A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells. + IEDB + IEDB + MIF release|cytometric bead array + cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells - + - + - - - - - + - + + + + + + + + + + + - A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody. - PERSON:Randi Vita, James Overton, Bjoern Peters - IEDB - qualitative binding|hydroxyl-radical footprinting assay - hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex + cytometric bead array assay measuring epitope specific oncostatin M production by T cells + + A cytometric bead array assay that detects oncostatin M production by T cells. + IEDB + IEDB + oncostatin M release|cytometric bead array + cytometric bead array assay measuring epitope specific oncostatin M production by T cells - + - + - + @@ -61596,7 +67807,7 @@ https://www.doi.org/ - + @@ -61610,18 +67821,20 @@ https://www.doi.org/ - An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNa release|ELISA - ELISA measuring epitope specific interferon-alpha production by T cells + ELISPOT assay measuring epitope specific perforin release by T cells + + An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells. + IEDB + IEDB + perforin release|ELISPOT + ELISPOT assay measuring epitope specific perforin release by T cells - + - + @@ -61634,7 +67847,7 @@ https://www.doi.org/ - + @@ -61645,535 +67858,10905 @@ https://www.doi.org/ + + + + + + + + + + + + + + + + + + + + + + + + - A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNa release|biological activity - assay measuring epitope specific interferon-alpha production by T cells - - - - - - - - - ‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension' - An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process. - Mathias Brochhausen - MIABIS2.0 - health status inclusion criterion - - - - - - - - - 'smoking behavior’ - An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process. - Mathias Brochhausen - MIABIS2.0 - clinically relevant lifestyle inclusion criterion + in vivo assay measuring epitope specific proliferation of T cells + + A T cell epitope specific proliferation assay that is performed in vivo. + IEDB + IEDB + proliferation|in vivo assay + in vivo assay measuring epitope specific proliferation of T cells - + - - - 'exposure to cigarette smoke’, ‘exposure to lead through drinking water' - An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process. - Mathias Brochhausen - MIABIS2.0 - clinically relevant exposure inclusion criterion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro assay measuring epitope specific proliferation of T cells + + A T cell epitope specific proliferation assay that is performed on cells in vitro. + IEDB + IEDB + proliferation|in vitro assay + in vitro assay measuring epitope specific proliferation of T cells - + - - - 'pregnant’, ‘not pregnant' - An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process. - Mathias Brochhausen - MIABIS2.0 - gravidity inclusion criterion + + + + + + + + + + + + + + + + + + + + + + assay measuring qualitative binding of a MHC:ligand complex + + An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output. + IEDB + IEDB + qualitative binding|binding assay + assay measuring qualitative binding of a MHC:ligand complex - + - - - - - - - - - An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. - Rebecca Jackson - PRO-Seq - precision nuclear run-on and sequencing assay - PMID:23430654 - https://github.com/obi-ontology/obi/issues/876 - precision nuclear run-on sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from challenge + + An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. + IEDB + IEDB + protection from challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection from challenge - + - - + + - - + + + + + + + + + + + + - A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. - Rebecca Jackson - 4C assay - circularized chromosome conformation capture assay - url:http://www.sciencedirect.com/science/article/pii/B9780123919380000045 - https://github.com/obi-ontology/obi/issues/875 - chromosome conformation capture-on-chip assay - - - - - - - - - + - - - - - - + + + + + + + + + - A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. - Rebecca Jackson - haplotype reconstruction by Hi-C assay - PMID:19815776 - url:https://www.nature.com/articles/nbt.2728 - https://github.com/obi-ontology/obi/issues/828 - genotype phasing by Hi-C assay - - - - - - - - - defined population inclusion criterion - inclusion based on age, sex, and living region (rural area or specified city). - An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. - Chris Stoeckert, Mathias Brochhausen - MIABIS 2.0 - 920 - MIABIS 2.0 - defined population inclusion criterion - - - - - - - - - BCL format - A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - BCL format + assay measuring T cell epitope specific suppression in vitro + + T cell epitope dependent biological activity assay that detects suppression of an in vitro response. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + suppression|in vitro assay + assay measuring T cell epitope specific suppression in vitro - + - - + + - + - - + + + + + + + + + + + + + + - - ERCC RNA spike-in - A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - https://www.thermofisher.com/order/catalog/product/4456740 - ERCC RNA spike-in + + MHC ligand assay + + An immune epitope assay that characterizes the structrue of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule. + IEDB + IEDB + MHC ligand assay|any method + MHC ligand assay - + - - + + - + - - + + - - SIRV RNA spike-in - A processed material that consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - https://www.lexogen.com/sirvs/design/ - SIRV RNA spike-in - - - - - - - - - SRS identifier - An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database. - Stephen Fisher, Dan Berrios - SRA sample accession number - SRS identifier + + + collection of specimens + Blood cells collected from multiple donors over the course of a study. + + A material entity that has two or more specimens as its parts. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert, Jie Zheng + OBIB, OBI + Biobank + collection of specimens - + - - - age since culture seeding measurement datum - An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). - Stephen A. Fisher, Junhyong Kim, Dan Berrios - age of culture - age since culture seeding measurement datum + + + specimens derived from shared ancestor + Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy. + + A collection of specimens derived from one common specimen via one or more material processing process(es). + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Chris Stoeckert, Jie Zheng + specimen family + Duke Biobank, OBIB, OBI + Biobank + specimens derived from shared ancestor - + - - - alignment counting algorithm - An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts). - Stephen A. Fisher, Junhyong Kim, Dan Berrios - alignment counting algorithm + + + specimen set collection process + Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy. + + A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. + Chris Stoeckert, Jie Zheng + OBIB, OBI + specimen set collection process - + - - - alignment counting application - A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - doi:10.1093/bioinformatics/btu638 - alignment counting application + + + specimens collected in one encounter + Both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy. + + A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert, Jie Zheng + specimen set + OBIB, OBI + Biobank + specimens collected in one encounter - + - - - base calling algorithm - An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer - Stephen A. Fisher, Junhyong Kim, Dan Berrios - base calling algorithm + + + + + + + + + + + + + + + + + + + human specimen set + + A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert, Jie Zheng + Duke Biobank, OBIB, OBI + Biobank + human specimen set - + - - - base calling application - A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - base calling application + + + specimens collected longitudinally + + A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity. + Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Person: Chris Stoeckert + Bjoern Peters, OBI + specimens collected longitudinally - + - - - bcl2fastq software application - A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html - bcl2fastq software application + + + reporter gene assay + + An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. + Chris Stoeckert + Paul D. Thomas + reporter gene detection assay + Paul D. Thomas, Yang Chai; FaceBase + https://github.com/obi-ontology/obi/issues/781 + reporter gene assay - + - - - date process started - A data item that is the date when a process was initiated. - Chris Stoeckert, Daniel Berrios, Stephen A. Fisher - date process started + + + enhancer activity detection by reporter gene assay + PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules" + + A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. + Paul D. Thomas + Yang Chai + enhancer reporter gene assay + FaceBase + PMID 24614317 + https://github.com/obi-ontology/obi/issues/781 + enhancer activity detection by reporter gene assay - + - - - dbGaP study identifier - A central registered identifier symbol that denotes a specific study in dbGaP. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - dbGaP accession number - doi:10.1038/ng1007-1181 - dbGaP study identifier + + + transcription cofactor activity region identification by ChIP-Seq assay + PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue" + + A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. + Paul D. Thomas + Yang Chai + chromatin modifier binding site identification by ChIP-Seq assay + PMID:19212405 + https://github.com/obi-ontology/obi/issues/782 + transcription cofactor activity region identification by ChIP-Seq assay - + - - - material amplification role - A worker role played by the person who runs the enzymatic amplifying process. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - material amplification role + + + transcript expression location detection by hybridization chain reaction assay + PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells" + + An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. + Paul D. Thomas + Yang Chai + transcript expression location detection by fluorescent HCR. + PMID:21037591 + https://github.com/obi-ontology/obi/issues/783 + transcript expression location detection by hybridization chain reaction assay - + - - - material sequencing library preparation role - A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - material sequencing library preparation role + + + Tet-assisted bisulfite sequencing assay + + A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected. + Bjoern Peters + Chris Stoeckert + Jason Hilton + OBI + TAB-seq + Tet-assisted bisulfite sequencing + PMID:23196972 + http://sourceforge.net/p/obi/obi-terms/789/ + Tet-assisted bisulfite sequencing assay - + - - - number of PCR cycles during library construction - A data item that is the number of PCR cycles used during the construction of a sequencing library. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - library construction PCR cycles - https://en.wikipedia.org/wiki/Polymerase_chain_reaction - number of PCR cycles during library construction + + + containing a specimen function + + A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay. + For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ + Chris Stoeckert + Duke Biobank, OBIB + Biobank + containing a specimen function - + - - - number of rounds of amplification - A data item that is the number of times an amplification reaction happened. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - number of rounds of amplification - + + + + + + + + + + + + + specimen container + COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube + + A container with the function of containing a specimen. + For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ + Chris Stoeckert + Duke Biobank, OBIB + specimen container + - + - - - reference genome role - A reference substance role that is played by a reference genome when used during sequence alignment. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - reference genome role + + + + + + + + + + + + + physical store + a freezer. a humidity controlled box. + + A container with an environmental control function. + For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ + Chris Stoeckert + Duke Biobank, OBIB + physical store - + - - - reference genome-transcriptome alignment algorithm - An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - reference genome-transcriptome alignment algorithm + + + rapid amplification of cDNA ends + + A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA. + For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ + Jason Hilton, Chris Stoeckert + RACE + http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/RACE_Rapid_Amplification_of_cDNA_Ends/5_Prime_RACE_and_3_Prime_RACE + ENCODE + rapid amplification of cDNA ends - + - - - sequence read length measurement datum - A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - read length, read length measurement datum - sequence read length measurement datum + + + 5' rapid amplification of cDNA ends + + A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 5' end of the mRNA. + For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ + Jason Hilton, Chris Stoeckert + 5' RACE + https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/5-race-system-for-rapid-amplification-of-cdna-ends.html + ENCODE + 5' rapid amplification of cDNA ends - + - - - sequencing library input quantity measurement datum - A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer. - Stephen A. Fisher, Junhyong Kim - library input amount - sequencing library input quantity measurement datum + + + 3' rapid amplification of cDNA ends + + A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 3' end of the mRNA. + For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ + Jason Hilton, Chris Stoeckert + 3' RACE + https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/3-race-system-for-rapid-amplification-of-cdna-ends.html + ENCODE + 3' rapid amplification of cDNA ends - + - - - single-end library - A cDNA library that is a collection of short tags from only one end of DNA fragments. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - single-end library + + + 5' RNA ligase mediated rapid amplification of cDNA ends + + A 5' rapid amplification pf cDNA ends that uses RNA ligase to add an RNA adapter oligonucleotide to intact 5' mRNA ends, allowing the amplification of cDNA only from full-length, capped mRNA. + For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ + Jason Hilton, Chris Stoeckert + 5' RLM RACE + https://tools.thermofisher.com/content/sfs/manuals/cms_056070.pdf + ENCODE + 5' RNA ligase mediated rapid amplification of cDNA ends - + - - - specimen harvest quantity - A scalar measurement datum that indicates the amount of specimen collected. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - harvest quantity - specimen harvest quantity + + + MethylC-Capture sequencing assay + MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants. + + A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. + Chris Stoeckert + David Bujold + Capture Methylome + MCC-Seq + MethylC-Capture Sequencing + PMID:26021296 + MethylC-Capture sequencing assay - + - - - spike-in dilution factor - A data item that indicates the dilution of spike-in added to a specimen. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - spike-in dilution factor + + + + + + + + + + + + + + + + + specimen family creation + Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum. + + A material processing that has as its input a specimen and as its output a collection of specimens. + For details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ + Mathias Brochhausen, Chris Stoeckert, Jie Zheng + OBI, OBIB + Biobank + specimen family creation - + - - - star algorithm - A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - https://www.ncbi.nlm.nih.gov/pubmed/23104886 - star algorithm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells + + A CFSE assay that detects T cell epitope specific proliferation in vitro. + IEDB + IEDB + proliferation|CFSE + carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells - + - - - A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. - Dan Berrios - Junhyong Kim - Stephen A. Fisher - transcript analysis by single-end sequencing - url:https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html - transcript analysis by single-end sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex + + A T cell epitope binding constant determination assay that measures the dissociation constant KD. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + dissociation constant KD|binding assay|nM + assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex - + - - - verse algorithm - An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. - Stephen A. Fisher, Junhyong Kim - http://kim.bio.upenn.edu/software/verse.shtml or http://biorxiv.org/content/early/2016/05/14/053306 - verse algorithm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex + + A T cell epitope binding constant determination assay that measures the on rate. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + on rate|binding assay|M^-1s^-1 + assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex - + - - - microraft - A material separation device also commerically known as Isoraft, that is used to isolate single cells. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - https://en.wikipedia.org/wiki/Microrafts - microraft + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex + + A T cell epitope binding constant determination assay that measures the off rate. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + off rate|binding assay|1/s + assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex + + A T cell epitope binding constant determination assay that measures the association constant KA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + association constant KA|binding assay|1/nM + assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex + + A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + 3D structure|small-angle scattering assay + small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex + + A bio-layer interferometry assay that measures the on rate of an antigen with an antibody. + IEDB + IEDB + on rate|bio-layer interferometry assay|M^-1s^-1 + bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex + + A bio-layer interferometry assay that measures the off rate of an antigen with an antibody. + IEDB + IEDB + off rate|bio-layer interferometry assay|1/s + bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex + + A bio-layer interferometry assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|bio-layer interferometry assay + bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody. + IEDB + IEDB + dissociation constant KD|bio-layer interferometry assay|nM + bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + + + carboxyfluorescein succinimidyl ester staining assay + Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division. + + a assay detecting a molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection. + IEDB + CFSE assay + IEDB + carboxyfluorescein succinimidyl ester staining assay + + + + + + + + + bio-layer interferometry assay + Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds. + + A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. + IEDB + biolayer interferometry, BLI + IEDB + bio-layer interferometry assay + + + + + + + + + small-angle scattering 3D molecular structure determination assay + Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein + + A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. + IEDB + SAXS + IEDB + small-angle scattering 3D molecular structure determination assay + + + + + + + + + + + + + + + Human 6x630K CGH Whole Genome Tiling Array + + A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. + Term request: https://sourceforge.net/p/obi/obi-terms/791/ + Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group + NimbleGen Human 6x630K CGH Whole Genome Tiling Array + http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 + Human 6x630K CGH Whole Genome Tiling Array + + + + + + + + + digital object identifier + The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 + + A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. + Discussed on Aug 22, 2016 OBI dev call. Details see tracker: +https://sourceforge.net/p/obi/obi-terms/818/ + OBI developers + DOI + https://en.wikipedia.org/wiki/Digital_object_identifier +https://www.doi.org/ + digital object identifier + + + + + + + + + enhanced cross-linking immunoprecipitation high-throughput sequencing assay + + An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. + Chris Stoeckert + Jason Hilton + eCLIP + PMID:27018577 + enhanced cross-linking immunoprecipitation high-throughput sequencing assay + + + + + + + + + small RNA sequencing assay + + An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. + Chris Stoeckert + Jason Hilton + Mark A. Miller + short RNA-seq + small RNA-seq + url:http://science.sciencemag.org/content/316/5830/1484.full + url:http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html + https://github.com/obi-ontology/obi/issues/859 + small RNA sequencing assay + + + + + + + + + bromouridine labeling and sequencing assay + + An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. + Chris Stoeckert + Jason Hilton + Bru-seq + PMC:4009065 + bromouridine labeling and sequencing assay + + + + + + + + + bromouridine pulse-chase and sequencing assay + + An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. + Chris Stoeckert + Jason Hilton + BruChase-seq + PMC:4009065 + bromouridine pulse-chase and sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometry time of flight assay + Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining refelctive of the level of expression of those surface receptors. + + A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. + ImmPort + CyTOF + mass cytometry assay + PMID:26190063 + cytometry time of flight assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + high performance liquid chromotography assay + On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. + + An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. + ImmPort + HPLC + PMID:9491555 + high performance liquid chromotography assay + + + + + + + + + whole genome sequencing assay + WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS. + + A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + ImmPort + WGS + PMID:23095910 + PMID:25827230 + whole genome sequencing assay + + + + + + + + + exome sequencing assay + DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified. + + A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). + ImmPort + WES + PMID:25827230 + exome sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + microscopy assay + Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy. + + An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. + ImmPort + PMID:21685355 + microscopy assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mixed lymphocyte reaction assay + T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells. + + A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators). + ImmPort + MLR + PMID:14969764 + mixed lymphocyte reaction assay + + + + + + + + + killer cell immunoglobulin-like receptor typing assay + DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself. + + A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + ImmPort + KIR typing + PMID:21239231 + killer cell immunoglobulin-like receptor typing assay + + + + + + + + + major histocompatibility typing assay + Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both_ according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size_ were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. + + A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. + Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. + IEDB + MHC typing, HLA typing + PMC:2628004 + PMID:27516207 + major histocompatibility typing assay + + + + + + + + + + + + + + + + + + + IHC slide staining + + A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues. + Chris Stoeckert, Ned Haubein + http://www.agilent.com/cs/library/technicaloverviews/public/08002_ihc_staining_methods.pdf + IHC slide staining + + + + + + + + + + + + + + + + + + + H&E slide staining + + A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink. + Chris Stoeckert, Ned Haubein + http://www.histalim.com/accueil/activities/our-services/histology/hematoxylin-eosin-2/ + H&E slide staining + + + + + + + + + + + + + + + + + + + H&E-stained fixed tissue slide specimen + + A fixed tissue slide specimen that is the output of H&E slide staining. + Chris Stoeckert, Ned Haubein + OBIB, OBI + H&E-stained fixed tissue slide specimen + + + + + + + + + + + + + + + + + + + IHC-stained fixed tissue slide specimen + + A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. + Chris Stoeckert, Ned Haubein + immunohistochemistry slide specimen + OBIB, OBI + IHC-stained fixed tissue slide specimen + + + + + + + + + single cell specimen + + A cell specimen that contains only one cell. + Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ + PERSON: Jie Zheng, Alexander Diehl + PERSON: Jie Zheng, Alexander Diehl + single cell specimen + + + + + + + + + Illumina Genome Analyzer + + A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. + Person: Chris Stoeckert, Jason Hilton + Illumina Genome Analyzer I + http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html + Illumina Genome Analyzer + + + + + + + + + Illumina HiSeq X Ten + + A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann + HiSeq X Ten + http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html + Illumina HiSeq X Ten + + + + + + + + + Illumina Infinium Omni5Exome-4 Kit + + An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. + Person: Chris Stoeckert, Jason Hilton + http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html + Illumina Infinium Omni5Exome-4 Kit + + + + + + + + + Illumina Infinium MethylationEPIC BeadChip + + An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. + Person: Chris Stoeckert, Jason Hilton + http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf + Illumina Infinium MethylationEPIC BeadChip + + + + + + + + + pulse stable isotope labeling by amino acids in cell culture + + An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability. + Rob Nash + dynamic SILAC + pulse SILAC + pulsed SILAC + PMID:18954100 + PMID:19053139 + pulse stable isotope labeling by amino acids in cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells + + A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + CCL20/MIP-3a release|cytometric bead array + cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells + + A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + CCL20/MIP-3a release|biological activity + assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + RNA Integrity Number calculation + + A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. + Chris Stoeckert, Bjoern Peters + RIN calculation + https://www.agilent.com/cs/library/applications/5989-1165EN.pdf + RNA Integrity Number calculation + + + + + + + + + RNA Integrity Number value specification + + A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). + Chris Stoeckert, Bjoern Peters + RIN value specification + OBI + RNA Integrity Number value specification + + + + + + + + + + + + + + + + + + + + + + + temperature value specification + + A value specification that specifies the temperature of some thing. + Chris Stoeckert + OBI + temperature value specification + + + + + + + + + + + + + + + + + + + + + + + volume value specification + + A value specification that specifies the volume of some thing. + Chris Stoeckert + OBI + volume value specification + + + + + + + + + + + + + + + + + + + + + + + + + temperature measurement assay + + An assay to determine the temperature of an evaluant. + Bjoern Peters + Chris Stoeckert + OBI + temperature measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + volume measurement assay + + An assay to determine the volume of an evaluant. + Bjoern Peters + Chris Stoeckert + OBI + volume measurement assay + + + + + + + + + Nanostring nCounter miRNA expression assay + + A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. + Chris Stoeckert + Jason Hilton + microRNA counts + PMID:26729350 + url:http://www.nanostring.com/applications/technology + https://github.com/obi-ontology/obi/issues/806 + ENCODE DCC + Nanostring nCounter miRNA expression assay + + + + + + + + + bromouride labeling and sequencing after UV exposure + + An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. + Chris Stoeckert + Jason Hilton + BruUV-seq + PMC:4675984 + https://github.com/obi-ontology/obi/issues/827 + ENCODE DCC + bromouride labeling and sequencing after UV exposure + + + + + + + + + extrachromosomal circular DNA sequencing assay + + An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. + Chris Stoeckert + Jason Hilton + circulome-seq + eccDNA-seq + url:http://biorxiv.org/content/early/2017/04/19/128686 + https://github.com/obi-ontology/obi/issues/830 + ENCODE DCC + extrachromosomal circular DNA sequencing assay + + + + + + + + + antigen specific antibodies assay + Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens + + An analyte assay that measures the presence or amount of antibodies to a specified antigen. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + antigen specific antibodies assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HIV antibody assay + + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. + HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36) + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HIV I/II Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + HIV antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HIV group O antibody assay + + An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. + https://www.cdc.gov/mmwr/preview/mmwrhtml/00042810.htm + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HIV I/II Plus O assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + HIV group O antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + surface HBV antibody assay + + An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HBsAb assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + surface HBV antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + core HBV antibody assay + + An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HBcAb assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + core HBV antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + core HBV IgM antibody assay + + An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HBcAb-IgM assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + core HBV IgM antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HCV antibody assay + + An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HCV Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + HCV antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EBV IgG antibody assay + + An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + EBV IgG Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + EBV IgG antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EBV IgM antibody assay + + An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + EBV IgM Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + EBV IgM antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CMV antibody assay + + An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + CMV Ab assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + CMV antibody assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + venereal disease research laboratory test + + An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + VDRL test + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + venereal disease research laboratory test + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + rapid plasma reagin test + + An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + RPR assay + url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/ + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + rapid plasma reagin test + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HBV surface antigen assay + + An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HBsAg assay + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + HBV surface antigen assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HIV-1 nucleic acid testing + + An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HIV-1 NAT + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + HIV-1 nucleic acid testing + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + HCV nucleic acid testing + + An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. + Bjoern Peters + Chris Stoeckert + James Overton + Randi Vita + HCV NAT + OBI + https://github.com/obi-ontology/obi/issues/825 + NCI BBRB + HCV nucleic acid testing + + + + + + + + + multiplexed indexed T7 ChIP-seq assay + + A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. + Chris Stoeckert + Jason Hilton + Mint-ChIP + Mint-ChIP-seq + url:http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00863-1 + https://github.com/obi-ontology/obi/issues/829 + ENCODE DCC + multiplexed indexed T7 ChIP-seq assay + + + + + + + + + systematic evolution of ligands by exponential enrichment assay + + A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ + Rebecca Jackson + SELEX + PMID:21720957 + systematic evolution of ligands by exponential enrichment assay + + + + + + + + + footprinting assay + + An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. + Bjoern Peters + doi:10.1002/3527600906.mcb.200300025 + footprinting assay + + + + + + + + + DNAse footprinting assay + + An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis + Rebecca Jackson + OBI development call + DNAse footprinting assay + + + + + + + + + mammalian 2-hybrid assay + + A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. + Rebecca Jackson + ECO:0001095 + PMID:9043710 + mammalian 2-hybrid assay + + + + + + + + + protein localization assay + + An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. + Rebecca Jackson + OBI development call + protein localization assay + + + + + + + + + tissue-based protein localization assay + + A protein localization assay that determines the specific location of a protein in a living tissue sample. + Rebecca Jackson + PMID:14686950 + tissue-based protein localization assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + subcellular protein localization assay + + A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. + Rebecca Jackson + ECO + subcellular protein localization assay + + + + + + + + + subcellular protein immunohistochemistry assay + + An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. + Rebecca Jackson + ECO + subcellular protein immunohistochemistry assay + + + + + + + + + + + + + + + + + + + + + + ChIP-qPCR assay + + A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. + Chris Stoeckert + PMID:18388953 + ChIP-qPCR assay + + + + + + + + + genomic SELEX + + A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. + Chris Stoeckert + PMID:20541015 + genomic SELEX + + + + + + + + + dot blot assay + + An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. + Bjoern Peters + dot blot analysis + PMID:10473518 + dot blot assay + + + + + + + + + Northwestern blot assay + + A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. + Bjoern Peters + Northwestern analysis + Northwestern assay + PMID:26965261 + Northwestern blot assay + + + + + + + + + Southwestern blot assay + + A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. + Bjoern Peters + PMID:26404144 + Southwestern blot assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + immunocytochemistry + + An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed + Bjoern Peters + immunocytochemistry + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ATP bioluminescence assay + + An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. + Rebecca Jackson + ATP quantitation assay + cell viability ATP quantitation assay + ECO + ATP bioluminescence assay + + + + + + + + + electrophysiology assay + + An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance). + Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues. + Gully Burns + url:https://en.wikipedia.org/wiki/Electrophysiology + electrophysiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + patch clamp assay + + An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations. + Gully Burns + ECO:0006012 + url:http://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.46.030184.002323 + url:https://en.wikipedia.org/wiki/Patch_clamp + patch clamp assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + whole-cell patch clamp assay + + A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. + Gully Burns + ECO:0006015 + url:https://en.wikipedia.org/wiki/Patch_clamp#Whole-cell_recording_or_whole-cell_patch + whole-cell patch clamp assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell-attached patch clamp assay + + A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. + Gully Burns + url:https://en.wikipedia.org/wiki/Patch_clamp#Cell-attached_patch + cell-attached patch clamp assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inside-out patch clamp assay + + A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations. + Gully Burns + url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ + url:https://en.wikipedia.org/wiki/Patch_clamp#Inside-out_patch + inside-out patch clamp assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outside-out patch clamp assay + + A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels. + Gully Burns + url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ + url:https://en.wikipedia.org/wiki/Patch_clamp#Outside-out_patch + outside-out patch clamp assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + voltage clamp assay + + An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. + Gully Burns + url:https://en.wikipedia.org/wiki/Voltage_clamp + voltage clamp assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + two electrode voltage clamp assay + + The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation. + Gully Burns + TEVC + url:https://en.wikipedia.org/wiki/Voltage_clamp#Two-electrode_voltage_clamp_using_microelectrodes + two electrode voltage clamp assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cut open oocyte voltage clamp assay + + The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques. + Gully Burns + COVG + PMID:9711615 + cut open oocyte voltage clamp assay + + + + + + + + + current clamp assay + + The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels. + Gully Burns + url:https://en.wikipedia.org/wiki/Electrophysiology#Current_clamp + current clamp assay + + + + + + + + + electroencephalography + + An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. + Gully Burns + EEG + electroencephalography + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + single-unit recording + + An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique. + Can be used on any cell, not just neurons. + Gully Burns + url:http://www.thieme.com/media/samples/pubid-80418214.pdf + single-unit recording + + + + + + + + + multi-unit recording + + An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. + Gully Burns + multi-unit recording + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + local field potential recording + + An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. + Gully Burns + doi:10.1007/978-1-4614-7320-6_723-1 + local field potential recording + + + + + + + + + + + + + + + + + + + + + + + + + courier organization + + An organization that delivers messages, packages, and mail. + Chris Stoeckert, Helena Ellis + courier + https://en.wikipedia.org/wiki/Courier + NCI BBRB + courier organization + + + + + + + + + courier tracking number + + A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + courier tracking number + + + + + + + + + Leica Peloris rapid tissue processor + + An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. + Chris Stoeckert, Helena Ellis + http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf + NCI BBRB + Leica Peloris rapid tissue processor + + + + + + + + + Microm Ergostar HM200 + + A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right. + Chris Stoeckert, Helena Ellis + http://www.ultra-medical.com/Microm-Ergostar-HM200-Microtome/en + NCI BBRB + Microm Ergostar HM200 + + + + + + + + + microtome blade + + A device that is the part of a microtome used to slice specimens to a desired thickness. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Microtome + NCI BBRB + microtome blade + + + + + + + + + Sakura Low profile Accu-Edge microtome blade + + A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering. + Chris Stoeckert, Helena Ellis + http://www.sakura.eu/Our-products/item/8/Microtomy/29/Accu-Edge-Disposable-Microtome-Blades + NCI BBRB + Sakura Low profile Accu-Edge microtome blade + + + + + + + + + tissue section thickness + + A length measurement datum that is the result of an assay measuring the thickness of a tissue section. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + tissue section thickness + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + molecular analysis facility organization + An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs. + + An organization that provides molecular analysis service. + Chris Stoeckert, Helena Ellis + MAF + NCI BBRB, OBIB + NCI BBRB + molecular analysis facility organization + + + + + + + + + reason for lack of data item + cannot be assessed, not applicable, unknown + + An information content entity that provides an explanation why a data item is not provided. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB + reason for lack of data item + + + + + + + + + cannot be assessed determination + + A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. + Chris Stoeckert, Helena Ellis + cannot be assessed + OBI + NCI BBRB + cannot be assessed determination + + + + + + + + + determination if assay will provide reliable results + + A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB + determination if assay will provide reliable results + + + + + + + + + GX + AJCC 7th edition GX: cannot be assessed. + + A cannot be assessed determination for histologic tumor grade. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB + GX + + + + + + + + + pTX + AJCC 7th edition pTX: cannot be assessed. + + A cannot be assessed determination for pathologic primary tumor staging. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB + pTX + + + + + + + + + pNX + AJCC 7th edition pNX: cannot be assessed. + + A cannot be assessed determination of pathologic staging of lymph nodes. + Chris Stoeckert, Helena Ellis + OBI + NCI BBRB + pNX + + + + + + + + + histologic grade according to AJCC 7th edition + G1:Well differentiated + G4: Undifferentiated + + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade according to AJCC 7th edition + + + + + + + + + histologic grade according to the Fuhrman Nuclear Grading System + + A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. + Chris Stoeckert, Helena Ellis + Histologic Grade (Fuhrman Nuclear Grading System) + NCI BBRB, OBI + NCI BBRB + histologic grade according to the Fuhrman Nuclear Grading System + + + + + + + + + histologic grade for ovarian tumor + + A categorical value specification that is a histologic grade assigned to a ovarian tumor. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor + + + + + + + + + histologic grade for ovarian tumor according to a two-tier grading system + + A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor according to a two-tier grading system + + + + + + + + + histologic grade for ovarian tumor according to the World Health Organization + + A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + histologic grade for ovarian tumor according to the World Health Organization + + + + + + + + + pathologic primary tumor stage for colon and rectum according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for colon and rectum according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread lung primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for lung according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic primary tumor stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic primary tumor stage for ovary according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for colon and rectum according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for colon and rectum according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for lung according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic lymph node stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. + Chris Stoeckert, Helena Ellis + pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic lymph node stage for ovary according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for colon according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: colon distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for colon according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for lung according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: lung distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for lung according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for kidney according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: kidney distant Metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for kidney according to AJCC 7th edition + + + + + + + + + pathologic distant metastases stage for ovary according to AJCC 7th edition + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. + Chris Stoeckert, Helena Ellis + M: ovarian distant metastases (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + pathologic distant metastases stage for ovary according to AJCC 7th edition + + + + + + + + + clinical tumor stage group according to AJCC 7th edition + + A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. + Chris Stoeckert, Helena Ellis + Clinical tumor stage group (AJCC 7th Edition) + NCI BBRB, OBI + NCI BBRB + clinical tumor stage group according to AJCC 7th edition + + + + + + + + + International Federation of Gynecology and Obstetrics cervical cancer stage value specification + + A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. + Chris Stoeckert, Helena Ellis + Clinical FIGO stage + NCI BBRB, OBI + NCI BBRB + International Federation of Gynecology and Obstetrics cervical cancer stage value specification + + + + + + + + + International Federation of Gynecology and Obstetrics ovarian cancer stage value specification + + A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. + Chris Stoeckert, Helena Ellis + Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) + NCI BBRB, OBI + NCI BBRB + International Federation of Gynecology and Obstetrics ovarian cancer stage value specification + + + + + + + + + performance status value specification + + A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). + Chris Stoeckert, Helena Ellis + Performance Status Scale + https://en.wikipedia.org/wiki/Performance_status + NCI BBRB + performance status value specification + + + + + + + + + Eastern Cooperative Oncology Group score value specification + + A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. + Chris Stoeckert, Helena Ellis + ECOG score + NCI BBRB, OBI + NCI BBRB + Eastern Cooperative Oncology Group score value specification + + + + + + + + + Karnofsky score vaue specification + + A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. + Chris Stoeckert, Helena Ellis + Karnofsky Score + NCI BBRB, OBI + NCI BBRB + Karnofsky score vaue specification + + + + + + + + + clinical history of cancer + + A clinical history in which there is a diagnosis of cancer. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + clinical history of cancer + + + + + + + + + clinical history devoid of cancer + + A clinical history in which there was no diagnosis of cancer. + Chris Stoeckert, Helena Ellis + clinical history of no cancer + NCI BBRB, OBIB + NCI BBRB + clinical history devoid of cancer + + + + + + + + + unknown clinical history of cancer + + A clinical history in which it is not known whether there was a diagnosis of cancer. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + unknown clinical history of cancer + + + + + + + + + diagnosis of cancer + + A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer. + Chris Stoeckert, Helena Ellis + cancer diagnosis + OBIB + NCI BBRB + diagnosis of cancer + + + + + + + + + family clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a blood relative. + Chris Stoeckert, Helena Ellis + family history of cancer + NCI BBRB, OBIB + NCI BBRB + family clinical history of cancer + + + + + + + + + aunt clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in the female sibling of a parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + aunt clinical history of cancer + + + + + + + + + brother clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a male sibling. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + brother clinical history of cancer + + + + + + + + + daughter clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a person's female child. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + daughter clinical history of cancer + + + + + + + + + father clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a male parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + father clinical history of cancer + + + + + + + + + mother clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a female parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + mother clinical history of cancer + + + + + + + + + sister clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a female sibling. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + sister clinical history of cancer + + + + + + + + + son clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a person's male child. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + son clinical history of cancer + + + + + + + + + uncle clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a male sibling of a parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + uncle clinical history of cancer + + + + + + + + + grandmother clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a female parent of a parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + grandmother clinical history of cancer + + + + + + + + + grandfather clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a male parent of a parent. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + grandfather clinical history of cancer + + + + + + + + + nephew clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a male child of a sibling. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + nephew clinical history of cancer + + + + + + + + + niece clinical history of cancer + + A clinical history in which there is a diagnosis of cancer in a female child of a sibling. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + niece clinical history of cancer + + + + + + + + + diagnosis of infectious disease + + A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + diagnosis of infectious disease + + + + + + + + + diagnosis of hepatitis B + + A diagnosis of infectious disease caused by the hepatitis B virus. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + diagnosis of hepatitis B + + + + + + + + + diagnosis of hepatitis C + + A diagnosis of infectious disease caused by the hepatitis C virus. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + diagnosis of hepatitis C + + + + + + + + + diagnosis of HIV + + A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + diagnosis of HIV + + + + + + + + + clinical history of repeated HIV assays + + A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + clinical history of repeated HIV assays + + + + + + + + + exposure to second hand smoke + + A clinical history in which there has been second hand exposure to tobacco smoking. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + exposure to second hand smoke + + + + + + + + + exposure to second hand smoke in household during childhood + + An exposure to second hand smoke that occurred in the (patient's) household when the person was a child. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + exposure to second hand smoke in household during childhood + + + + + + + + + exposure to second hand smoke in current household + + An exposure to second hand smoke in person's current household. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + exposure to second hand smoke in current household + + + + + + + + + pregnancy history + + A clinical history in which a female has had a pregnancy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + pregnancy history + + + + + + + + + number of pregnancies + + A measurement datum of the total number of pregnancies a woman has had. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + number of pregnancies + + + + + + + + + number of live births + + A measurement datum of the total number of live births a female has had. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + number of live births + + + + + + + + + age when gave birth to first child + + An age measurement datum performed on a female when her first biological child was born. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + age when gave birth to first child + + + + + + + + + gynecologic surgery history + + A clinical history in which a woman has had gynecologic surgery in the past. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + gynecologic surgery history + + + + + + + + + hysterectomy history + + A gynecologic surgery history in which a woman has had a hysterectomy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + hysterectomy history + + + + + + + + + unilateral oophorectomy history + + A gynecologic surgery history in which a woman has had a unilateral oophorectomy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + unilateral oophorectomy history + + + + + + + + + neither hysterectomy nor oophorectomy history + + A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + neither hysterectomy nor oophorectomy history + + + + + + + + + hormonal birth control use history + + An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + hormonal birth control use history + + + + + + + + + hormonal birth control former use history + + A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + hormonal birth control former use history + + + + + + + + + hormonal birth control current use history + + A hormonal birth control use history that indicates an individual is currently a hormonal birth control user. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + hormonal birth control current use history + + + + + + + + + no hormonal birth control use history + + A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + no hormonal birth control use history + + + + + + + + + hormonal replacement therapy history + + A clinical history in which an individual has had hormonal replacement therapy in the past. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + hormonal replacement therapy history + + + + + + + + + delivery form for hormonal replacement therapy + + A processed material used for delivery of hormones in hormone replacement therapy. + Chris Stoeckert, Helena Ellis + form of hormone replacement therapy + NCI BBRB, OBIB + NCI BBRB + delivery form for hormonal replacement therapy + + + + + + + + + pill delivery form for hormonal replacement therapy + + A delivery form for hormonal replacement therapy that is a pill for oral administration. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + pill delivery form for hormonal replacement therapy + + + + + + + + + patch delivery form for hormonal replacement therapy + + A delivery form for hormonal replacement therapy that is a patch for transdermal administration. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + patch delivery form for hormonal replacement therapy + + + + + + + + + cream delivery form for hormonal replacement therapy + + A delivery form for hormonal replacement therapy that is a cream for transdermal administration. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + cream delivery form for hormonal replacement therapy + + + + + + + + + menopausal status + + An information content entity that indicates the state of a female's cessation of menstruation. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + menopausal status + + + + + + + + + indeterminate menopausal status + + A menopausal status that is neither pre- nor post-menopausal. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + indeterminate menopausal status + + + + + + + + + premenopausal status + + A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + premenopausal status + + + + + + + + + perimenopausal status + + A menopausal status indicating that it has been 6-12 months since last menstrual period. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + perimenopausal status + + + + + + + + + postmenopausal status + + A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + postmenopausal status + + + + + + + + + exposure to environmental and workplace carcinogens history + + An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + exposure to environmental and workplace carcinogens history + + + + + + + + + exposure to arsenic history + + An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + exposure to arsenic history + + + + + + + + + exposure to asbestos history + + An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + exposure to asbestos history + + + + + + + + + exposure to diesel exhaust history + + An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + exposure to diesel exhaust history + + + + + + + + + exposure to chromium history + + An exposure to environmental and workplace carcinogens history where the carcinogen is chromium. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + exposure to chromium history + + + + + + + + + exposure to silica history + + An exposure to environmental and workplace carcinogens history where the carcinogen is silica. + Chris Stoeckert, Helena Ellis + OBIB + NCI BBRB + exposure to silica history + + + + + + + + + indicator of whether an inclusion criterion was met + + An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process. + Chris Stoeckert, Helena Ellis + eligibility criterion met + NCI BBRB, OBIB + NCI BBRB + indicator of whether an inclusion criterion was met + + + + + + + + + indicator of whether all inclusion criteria were met + + An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process. + Chris Stoeckert, Helena Ellis + all eligibility criteria met + NCI BBRB, OBIB + NCI BBRB + indicator of whether all inclusion criteria were met + + + + + + + + + age of majority inclusion criterion + + An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + age of majority inclusion criterion + + + + + + + + + chemotherapy treatment exclusion criterion + + An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + chemotherapy treatment exclusion criterion + + + + + + + + + radiation treatment exclusion criteria + + An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + radiation treatment exclusion criteria + + + + + + + + + chemotherapy treatment within the recent past exclusion criterion + An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years. + + An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + chemotherapy treatment within the recent past exclusion criterion + + + + + + + + + radiation treatment within the recent past exclusion criterion + An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years. + + An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + radiation treatment within the recent past exclusion criterion + + + + + + + + + BMI range inclusion criterion + An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0 + + An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + BMI range inclusion criterion + + + + + + + + + blood transfusion exclusion criterion + An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death. + + An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + blood transfusion exclusion criterion + + + + + + + + + history of metastatic cancer exclusion criterion + + An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + history of metastatic cancer exclusion criterion + + + + + + + + + intravenous drug use exclusion criterion + Donor eligibility based on history of intravenous drug abuse in the last 5 years. + + An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + intravenous drug use exclusion criterion + + + + + + + + + history of sex with someone with a history of blood borne infection exclusion criterion + Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years. + + An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + history of sex with someone with a history of blood borne infection exclusion criterion + + + + + + + + + history of sex with someone with a history of intravenous drugs exclusion criterion + Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years. + + An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + history of sex with someone with a history of intravenous drugs exclusion criterion + + + + + + + + + HIV exclusion criterion + + An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + HIV exclusion criterion + + + + + + + + + exposure to blood borne infectious disease exclusion criterion + Donor eligibility based on whether the donor has been exposed to HIV/AIDS. + + An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBIB + NCI BBRB + exposure to blood borne infectious disease exclusion criterion + + + + + + + + + + + + + + + + + + + + + + RNA interactome capture + + An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. + Rebecca Jackson + PMID:26463381 + RNA interactome capture + + + + + + + + + widefield microscopy assay + + A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. + Jie Zheng + WFM + url:http://bitesizebio.com/19409/the-many-flavors-of-widefield-microscopy/ + url:https://svi.nl/WideFieldMicroscope + widefield microscopy assay + + + + + + + + + + + + + + + + + + + + + nuclear ligation assay + + An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. + Chris S + PMID:8327891 + nuclear ligation assay + + + + + + + + + + + + + + + chromosome conformation capture assay + + A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. + Chris S + 3C assay + PMID:11847345 + url:http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.243.html + chromosome conformation capture assay + + + + + + + + + + + + + + + + + + + + + + Hi-C assay + + A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. + Chris S + PMID:20461051 + Hi-C assay + + + + + + + + + physical examination of individual + + An assay that produces a description of the qualities of an entity that has not been transformed, through observation and physical, non-invasive techniques. + physical examination of individual + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + hydroxyl-radical footprinting assay + + A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. + Jie Zheng + PMID:21770468 + hydroxyl-radical footprinting assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + methidiumpropyl-EDTA-iron(II) footprinting assay + + A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. + Jie Zheng + MPE-Fe(II) footprinting + PMID:6225070 + PMID:6435669 + methidiumpropyl-EDTA-iron(II) footprinting assay + + + + + + + + + + + + + + + measurand role + + A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. + Person: Alan Ruttenberg, Jie Zheng + https://en.wiktionary.org/wiki/measurand + https://github.com/obi-ontology/obi/issues/778 + measurand role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transcription start site mapping by primer extension assay + + A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. + Rebecca Jackson + PMID:23378648 + url:https://en.wikipedia.org/wiki/Primer_extension + transcription start site mapping by primer extension assay + + + + + + + + + proteomic profiling design + + A study design in which proteins in a sample are detected, quantified or otherwise analysed. + Dan Berrios + OBI:0001441 + proteomic profiling design + + + + + + + + + suppression subtractive hybridization + + An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library. + Rebecca Jackson + SSH + subtractive hybridization + PMID:14970460 + suppression subtractive hybridization + + + + + + + + + differential screening hybridization + + An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. + Rebecca Jackson + DSH + differential screening + PMID:25472628 + differential screening hybridization + + + + + + + + + + + + + + + + + + + + + + + + + + + + footprinting assay measuring binding of a B cell epitope:antibody complex + + A footprinting assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + qualitative binding|footprinting assay + footprinting assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex + + A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody. + PERSON:Randi Vita, James Overton, Bjoern Peters + IEDB + qualitative binding|hydroxyl-radical footprinting assay + hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interferon-alpha production by T cells + + An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNa release|ELISA + ELISA measuring epitope specific interferon-alpha production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring epitope specific interferon-alpha production by T cells + + A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNa release|biological activity + assay measuring epitope specific interferon-alpha production by T cells + + + + + + + + + health status inclusion criterion + ‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension' + + An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process. + Mathias Brochhausen + MIABIS2.0 + health status inclusion criterion + + + + + + + + + clinically relevant lifestyle inclusion criterion + 'smoking behavior’ + + An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process. + Mathias Brochhausen + MIABIS2.0 + clinically relevant lifestyle inclusion criterion + + + + + + + + + clinically relevant exposure inclusion criterion + 'exposure to cigarette smoke’, ‘exposure to lead through drinking water' + + An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process. + Mathias Brochhausen + MIABIS2.0 + clinically relevant exposure inclusion criterion + + + + + + + + + gravidity inclusion criterion + 'pregnant’, ‘not pregnant' + + An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process. + Mathias Brochhausen + MIABIS2.0 + gravidity inclusion criterion + + + + + + + + + + + + + + + precision nuclear run-on sequencing assay + + An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. + Rebecca Jackson + PRO-Seq + precision nuclear run-on and sequencing assay + PMID:23430654 + https://github.com/obi-ontology/obi/issues/876 + precision nuclear run-on sequencing assay + + + + + + + + + + + + + + + chromosome conformation capture-on-chip assay + + A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. + Rebecca Jackson + 4C assay + circularized chromosome conformation capture assay + url:http://www.sciencedirect.com/science/article/pii/B9780123919380000045 + https://github.com/obi-ontology/obi/issues/875 + chromosome conformation capture-on-chip assay + + + + + + + + + + + + + + + + + + + + + + genotype phasing by Hi-C assay + + A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. + Rebecca Jackson + haplotype reconstruction by Hi-C assay + PMID:19815776 + url:https://www.nature.com/articles/nbt.2728 + https://github.com/obi-ontology/obi/issues/828 + genotype phasing by Hi-C assay + + + + + + + + + defined population inclusion criterion + inclusion based on age, sex, and living region (rural area or specified city). + + An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. + Chris Stoeckert, Mathias Brochhausen + MIABIS 2.0 + https://github.com/obi-ontology/obi/issues/920 + MIABIS 2.0 + defined population inclusion criterion + + + + + + + + + BCL format + + A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + BCL format + + + + + + + + + + + + + + + + + + + ERCC RNA spike-in + + A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://www.thermofisher.com/order/catalog/product/4456740 + ERCC RNA spike-in + + + + + + + + + + + + + + + + + + + SIRV RNA spike-in + + A processed material that consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://www.lexogen.com/sirvs/design/ + SIRV RNA spike-in + + + + + + + + + SRS identifier + + An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database. + Stephen Fisher, Dan Berrios + SRA sample accession number + SRS identifier + + + + + + + + + age since culture seeding measurement datum + + An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). + Stephen A. Fisher, Junhyong Kim, Dan Berrios + age of culture + age since culture seeding measurement datum + + + + + + + + + alignment counting algorithm + + An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts). + Stephen A. Fisher, Junhyong Kim, Dan Berrios + alignment counting algorithm + + + + + + + + + alignment counting application + + A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + doi:10.1093/bioinformatics/btu638 + alignment counting application + + + + + + + + + base calling algorithm + + An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer + Stephen A. Fisher, Junhyong Kim, Dan Berrios + base calling algorithm + + + + + + + + + base calling application + + A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + base calling application + + + + + + + + + bcl2fastq software application + + A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html + bcl2fastq software application + + + + + + + + + date process started + + A data item that is the date when a process was initiated. + Chris Stoeckert, Daniel Berrios, Stephen A. Fisher + date process started + + + + + + + + + dbGaP study identifier + + A central registered identifier symbol that denotes a specific study in dbGaP. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + dbGaP accession number + doi:10.1038/ng1007-1181 + dbGaP study identifier + + + + + + + + + material amplification role + + A worker role played by the person who runs the enzymatic amplifying process. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + material amplification role + + + + + + + + + material sequencing library preparation role + + A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + material sequencing library preparation role + + + + + + + + + number of PCR cycles during library construction + + A data item that is the number of PCR cycles used during the construction of a sequencing library. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + library construction PCR cycles + https://en.wikipedia.org/wiki/Polymerase_chain_reaction + number of PCR cycles during library construction + + + + + + + + + number of rounds of amplification + + A data item that is the number of times an amplification reaction happened. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + number of rounds of amplification + + + + + + + + + reference genome role + + A reference substance role that is played by a reference genome when used during sequence alignment. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + reference genome role + + + + + + + + + reference genome-transcriptome alignment algorithm + + An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + reference genome-transcriptome alignment algorithm + + + + + + + + + sequence read length measurement datum + + A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + read length, read length measurement datum + sequence read length measurement datum + + + + + + + + + sequencing library input quantity measurement datum + + A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer. + Stephen A. Fisher, Junhyong Kim + library input amount + sequencing library input quantity measurement datum + + + + + + + + + single-end library + + A cDNA library that is a collection of short tags from only one end of DNA fragments. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + single-end library + + + + + + + + + specimen harvest quantity + + A scalar measurement datum that indicates the amount of specimen collected. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + harvest quantity + specimen harvest quantity + + + + + + + + + spike-in dilution factor + + A data item that indicates the dilution of spike-in added to a specimen. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + spike-in dilution factor + + + + + + + + + star algorithm + + A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://www.ncbi.nlm.nih.gov/pubmed/23104886 + star algorithm + + + + + + + + + transcript analysis by single-end sequencing assay + + A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. + Dan Berrios + Junhyong Kim + Stephen A. Fisher + transcript analysis by single-end sequencing + url:https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html + transcript analysis by single-end sequencing assay + + + + + + + + + verse algorithm + + An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. + Stephen A. Fisher, Junhyong Kim + http://kim.bio.upenn.edu/software/verse.shtml or http://biorxiv.org/content/early/2016/05/14/053306 + verse algorithm + + + + + + + + + microraft + + A material separation device also commerically known as Isoraft, that is used to isolate single cells. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://en.wikipedia.org/wiki/Microrafts + microraft + + + + + + + + + pipette + + A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. + Stephen A. Fisher, Junhyong Kim, Dan Berrios + https://en.wikipedia.org/wiki/Pipette + pipette + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + differential medium assay + + an organism identification assay that uses a differential medium to achieve its objective + John Judkins + bacteriological assay + EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm + differential medium assay + + + + + + + + + medication time value specification + + A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material + John Judkins + medication timepoint + OBI + VEuPathDB + medication time value specification + + + + + + + + + medication dose value specification + + A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment + John Judkins + medication dose + OBI + VEuPathDB + medication dose value specification + + + + + + + + + case role in case-control study + + A role that is borne by a case-control study design participant under investigation that is associated with the outcome mentioned in the study design. + John Judkins, Bjoern Peters + OBI + case role in case-control study + + + + + + + + + control role in case-control study + + A role that is borne by a case-control study design participant under investigation that is not associated with the outcome mentioned in the study design. + John Judkins, Bjoern Peters + OBI + control role in case-control study + + + + + + + + + + + + + + + + + + + + + + + amniotic fluid specimen + + A specimen that is derived from amniotic fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + amniotic fluid specimen + + + + + + + + + + + + + + + + + + + + + + + bile specimen + + A specimen that is derived from bile. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + bile specimen + + + + + + + + + + + + + + + + + + + + + + + cerebrospinal fluid specimen + + A specimen that is derived from cerbrospinal fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + cerebrospinal fluid specimen + + + + + + + + + + + + + + + + + + + + + + + feces specimen + + A specimen that is derived from feces. + Chris Stoeckert + stool specimen + Chris Stoeckert, Penn Medicine Biobank + feces specimen + + + + + + + + + + + + + + + + + + + + + + + digestive system fluid or secretion specimen + + A specimen that is derived from digestive system fluid or secretion. + Chris Stoeckert + gastric fluid specimen + Chris Stoeckert, Penn Medicine Biobank + digestive system fluid or secretion specimen + + + + + + + + + + + + + + + + + + + + + + + milk specimen + + A specimen that is derived from milk. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + milk specimen + + + + + + + + + + + + + + + + + + + + + + + pericardial fluid specimen + + A specimen that is derived from pericardial fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + pericardial fluid specimen + + + + + + + + + + + + + + + + + + + + + + + saliva specimen + + A specimen that is derived from saliva. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + saliva specimen + + + + + + + + + + + + + + + + + + + + + + + sputum specimen + + A specimen that is derived from sputum. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + sputum specimen + + + + + + + + + + + + + + + + + + + + + + + sweat specimen + + A specimen that is derived from sweat. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + sweat specimen + + + + + + + + + + + + + + + + + + + + + + + synovial fluid specimen + + A specimen that is derived from synovial fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + synovial fluid specimen + + + + + + + + + + + + + + + + + + + + + + + vitreous humor specimen + + A specimen that is derived from vireous humor. + Chris Stoeckert + vitreous fluid specimen + Chris Stoeckert, Penn Medicine Biobank + vitreous humor specimen + + + + + + + + + + + + + + + + + + + + + + + bone marrow specimen + + A specimen that is derived from bone marrow. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + bone marrow specimen + + + + + + + + + + + + + + + + + + + + + + + placenta specimen + + A specimen that is derived from placenta. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + placenta specimen + + + + + + + + + + + + + + + + + + + + + + + peritoneal fluid specimen + + A specimen that is derived from peritoneal fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + peritoneal fluid specimen + + + + + + + + + + + + + + + + + + + + + + + pleural fluid specimen + + A specimen that is derived from pleural fluid. + Chris Stoeckert + Chris Stoeckert, Penn Medicine Biobank + pleural fluid specimen + + + + + + + + + + + + + + + + + + + + + + + brain specimen + + A specimen that is derived from brain. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + brain specimen + + + + + + + + + + + + + + + + + + + + + + + hair specimen + + A specimen that is derived from hair. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + hair specimen + + + + + + + + + + + + + + + + + + + + + + + prostate gland specimen + + A specimen that is derived from prostate gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + prostate gland specimen + + + + + + + + + + + + + + + + + + + + + + + skeletal muscle tissue specimen + + A specimen that is derived from skeletal muscle. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + skeletal muscle tissue specimen + + + + + + + + + + + + + + + + + + + + + + + heart specimen + + A specimen that is derived from heart. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + heart specimen + + + + + + + + + + + + + + + + + + + + + + + renal medulla specimen + + A specimen that is derived from renal medulla. + Chris Stoeckert + kidney medulla specimen + Chris Stoeckert, NCI BBRB + renal medulla specimen + + + + + + + + + + + + + + + + + + + + + + + adrenal gland specimen + + A specimen that is derived from adrenal gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + adrenal gland specimen + + + + + + + + + + + + + + + + + + + + + + + breast specimen + + A specimen that is derived from breast. + Chris Stoeckert + mammary tissue specimen + Chris Stoeckert, NCI BBRB + breast specimen + + + + + + + + + + + + + + + + + + + + + + + urinary bladder specimen + + A specimen that is derived from urinary bladder. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + urinary bladder specimen + + + + + + + + + + + + + + + + + + + + + + + tibial artery specimen + + A specimen that is derived from tibial artery. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + tibial artery specimen + + + + + + + + + + + + + + + + + + + + + + + skin of body specimen + + A specimen that is derived from skin. + Chris Stoeckert + skin specimen + Chris Stoeckert, NCI BBRB + skin of body specimen + + + + + + + + + + + + + + + + + + + + + + + pancreas specimen + + A specimen that is derived from pancreas. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + pancreas specimen + + + + + + + + + + + + + + + + + + + + + + + stomach specimen + + A specimen that is derived from stomach. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + stomach specimen + + + + + + + + + + + + + + + + + + + + + + + pituitary gland specimen + + A specimen that is derived from pituitary gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + pituitary gland specimen + + + + + + + + + + + + + + + + + + + + + + + adipose tissue specimen + + A specimen that is derived from adipose tissue. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + adipose tissue specimen + + + + + + + + + + + + + + + + + + + + + + + cortex of kidney specimen + + A specimen that is derived from cortex of kidney. + Chris Stoeckert + kidney cortex specimen + Chris Stoeckert, NCI BBRB + cortex of kidney specimen + + + + + + + + + + + + + + + + + + + + + + + esophagus mucosa specimen + + A specimen that is derived from esophagus mucosa. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + esophagus mucosa specimen + + + + + + + + + + + + + + + + + + + + + + + colon specimen + + A specimen that is derived from colon. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + colon specimen + + + + + + + + + + + + + + + + + + + + + + + lung specimen + + A specimen that is derived from lung. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + lung specimen + + + + + + + + + + + + + + + + + + + + + + + esophagus muscularis mucosa specimen + + A specimen that is derived from esophagus muscularis mucosa. + Chris Stoeckert + esophagus muscularis specimen + Chris Stoeckert, NCI BBRB + esophagus muscularis mucosa specimen + + + + + + + + + + + + + + + + + + + + + + + cerebral cortex specimen + + A specimen that is derived from cerebral cortex. + Chris Stoeckert + brain cortex specimen + Chris Stoeckert, NCI BBRB + cerebral cortex specimen + + + + + + + + + + + + + + + + + + + + + + + thyroid gland specimen + + A specimen that is derived from thyroid gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + thyroid gland specimen + + + + + + + + + + + + + + + + + + + + + + + cerebellum specimen + + A specimen that is derived from cerebellum. + Chris Stoeckert + brain cerebellum specimen + Chris Stoeckert, NCI BBRB + cerebellum specimen + + + + + + + + + + + + + + + + + + + + + + + tibial nerve specimen + + A specimen that is derived from tibial nerve. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + tibial nerve specimen + + + + + + + + + + + + + + + + + + + + + + + coronary artery specimen + + A specimen that is derived from coronary artery. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + coronary artery specimen + + + + + + + + + + + + + + + + + + + + + + + spleen specimen + + A specimen that is derived from spleen. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + spleen specimen + + + + + + + + + + + + + + + + + + + + + + + aorta specimen + + A specimen that is derived from aorta. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + aorta specimen + + + + + + + + + + + + + + + + + + + + + + + atrial appendage specimen + + A specimen that is derived from the atrium auricular region. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + atrial appendage specimen + + + + + + + + + + + + + + + + + + + + + + + esophagogastric junction specimen + + A specimen that is derived from the esophagogastric junction. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + esophagogastric junction specimen + + + + + + + + + + + + + + + + + + + + + + + ileum specimen + + A specimen that is derived from ileum. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + ileum specimen + + + + + + + + + + + + + + + + + + + + + + + liver specimen + + A specimen that is derived from liver. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + liver specimen + + + + + + + + + + + + + + + + + + + + + + + minor salivary gland specimen + + A specimen that is derived from minor salivary gland. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + minor salivary gland specimen + + + + + + + + + + + + + + + + + + + + + + + omentum specimen + + A specimen that is derived from omentum. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + omentum specimen + + + + + + + + + + + + + + + + + + + + + + + ovary specimen + + A specimen that is derived from female gonad. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + ovary specimen + + + + + + + + + + + + + + + + + + + + + + + sigmoid colon specimen + + A specimen that is derived from sigmoid colon. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + sigmoid colon specimen + + + + + + + + + + + + + + + + + + + + + + + suprapubic skin specimen + + A specimen that is derived from suprapubic skin. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + suprapubic skin specimen + + + + + + + + + + + + + + + + + + + + + + + testis specimen + + A specimen that is derived from testis. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + testis specimen + + + + + + + + + + + + + + + + + + + + + + + uterus specimen + + A specimen that is derived from uterus. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + uterus specimen + + + + + + + + + + + + + + + + + + + + + + + vagina specimen + + A specimen that is derived from vagina. + Chris Stoeckert + Chris Stoeckert, NCI BBRB + vagina specimen + + + + + + + + + + + + + + + + + + + + + + + age group inclusion criterion + "18-33 years old" + + An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. + Mathias Brochhausen + https://github.com/obi-ontology/obi/issues/839 + age group inclusion criterion + + + + + + + + + minimum age value specification + + A value specifcation that specifies the youngest age when specifying an age range. + Mathias Brochhausen + minimum age value specification + + + + + + + + + maximum age value specification + + A value specifcation that specifies the oldest age when specifying an age range. + Mathias Brochhausen + maximum age value specification + + + + + + + + + use of medication inclusion criterion + "received at least 2 days of vancomycin" + + An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process. + Mathias Brochhausen + https://github.com/obi-ontology/obi/issues/840 + use of medication inclusion criterion + + + + + + + + + hospital patient inclusion criterion + "included hospital patients" + + An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process. + Mathias Brochhausen + hospital patient inclusion criterion + + + + + + + + + family status inclusion criterion + "included married and unmarried patients", "included divorced individuals" + + An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process. + Mathias Brochhausen + family status inclusion criterion + + + + + + + + + sex inclusion criterion + "included males and females", "included male patients" + + An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process. + Mathias Brochhausen + sex inclusion criterion + + + + + + + + + country of residence inclusion criteria + "include US residents" + + An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process. + Mathias Brochhausen + country of residence inclusion criteria + + + + + + + + + ethnicity inclusion criterion + "include only Hispanic individuals" + + An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process. + Mathias Brochhausen + ethnicity inclusion criterion + + + + + + + + + histopathology assay + + A histological assay that is intended to check for the presence or level of a specific disease. + OBI + histopathology assay + + + + + + + + + + + + + + + + + + + + + adapter-sequence trimming + + A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). + Dan Berrios + Dan Berrios + adapter-sequence trimming + + + + + + + + + file merge + + A data transformation in which data contained in 2 or more files are merged into a single file. + Dan Berrios + Dan Berrios + file merge + + + + + + + + + + + + + + + + + + + + + sequence alignment + + A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. + Dan Berrios + Dan Berrios + sequence alignment + + + + + + + + + + + + + + + + + + + + + sequence data feature count tabulation + + The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables. + Dan Berrios + Dan Berrios + sequence data feature count tabulation + + + + + + + + + + + + + + + + + + + trimmed sequence data + + The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective. + Dan Berrios + Dan Berrios + trimmed sequence data + + + + + + + + + + + + + + + nCounter Mouse miRNA Expression array + Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 + + A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 + https://www.nanostring.com/products/mirna-assays/mirna-panels + nCounter Mouse miRNA Expression array + + + + + + + + + + + + + + + polyA-selected RNA sequencing assay + + An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. + Jason Hilton + Mark A. Miller + mRNA-seq + url:https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-419 + ENCODE + polyA-selected RNA sequencing assay + + + + + + + + + + + + + + + polyA-depleted RNA sequencing assay + + An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. + Jason Hilton + Mark A. Miller + polyA-depleted RNA-seq + url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030733 + url:http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1110676 + ENCODE + polyA-depleted RNA sequencing assay + + + + + + + + + + + + + + + polyA depleted RNA extract + + A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. + Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 + PERSON: Chris Stoeckert + PERSON: Jie Zheng + UPenn Group + 2018-05-11T16:35:11Z + polyA depleted RNA extract + + + + + + + + + RNA extraction with polyA depletion + + A RNA extraction process in which only RNAs lacking a polyA tail are retained + Mark A. Miller, based on OBI_0000848 + UPenn Group + 2018-05-11T15:01:14Z + RNA extraction with polyA depletion + + + + + + + + + isoform sequencing + Novel transcript forms were assessed by isoform sequencing. + + A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. + ISO-seq + url:http://www.pacb.com/blog/intro-to-iso-seq-method-full-leng/ + isoform sequencing + + + + + + + + + adapter sequence data + + Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run. + Dan Berrios + Dan Berrios + adapter sequence data + + + + + + + + + adapter-trimmed sequence data + + The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. + Dan Berrios + Dan Berrios + adapter-trimmed sequence data + + + + + + + + + aligned sequence data + + The results of a sequence alignment. + Dan Berrios + Dan Berrios + aligned sequence data + + + + + + + + + + + + + + + merged aligned sequence data + + The results of a data transformation of sequence data in which files containing aligned sequence data are merged together + Dan Berrios + Dan Berrios + merged aligned sequence data + + + + + + + + + sequence library feature count data + + The results of a sequence data feature count tabulation. + Dan Berrios + Dan Berrios + sequence library feature count data + + + + + + + + + + + + + + + DNA methylation profiling data + + The results of a DNA methylation profiling assay + DNA methylation profiling data + + + + + + + + + differential expression analysis data + + The results of a differential expression analysis. + differential expression analysis data + + + + + + + + + sequence trimming + + A data transformation in which subsequences of a molecular sequence are cut (removed). + sequence trimming + + + + + + + + + + + + + + + digital acquisition card + + The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device). + Mark A. Miller + DAQ device + digital acquisition and digital generation card + Brenda Farrell, bfarrell@bcm.edu + digital acquisition card + + + + + + + + + machine learning + + A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task. + Mark A. Miller + https://en.wikipedia.org/wiki/Machine_learning + https://github.com/TrisSN + machine learning + + + + + + + + + supervised machine learning + + A machine learning process using a function that maps an input to an output based on example input-output pairs. It infers a function from labeled training data consisting of a set of training examples. + Mark A. Miller + https://en.wikipedia.org/wiki/Supervised_learning + https://github.com/TrisSN + supervised machine learning + + + + + + + + + unsupervised machine learning + + A machine learning process that infers a function describing the structure of "unlabeled" data (i.e. data that has not been classified or categorized). + Mark A. Miller + https://en.wikipedia.org/wiki/Unsupervised_learning + https://github.com/TrisSN + unsupervised machine learning + + + + + + + + + + + + + + + molecular interaction identification design + + A study design that investigates the features of interaction between molecules. + Rebecca Jackson + person:RCT + molecular interaction identification design + + + + + + + + + colocalization identification design + + A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules. + Rebecca Jackson + url:https://en.wikipedia.org/wiki/Colocalization + colocalization identification design + + + + + + + + + + + + + + + + + + + + + + + + + genetic interaction identification design + + A molecular interaction identification design that investigates a phenotype that is the result of two or more genetic perturbations, and is not explained by the individual genetic perturbations alone. + Rebecca Jackson + MI:0208 + genetic interaction identification design + + + + + + + + + functional association identification design + + A molecular interaction identification design that investigates a relationship that is the result of intermediate steps between two or more molecules that are not necessarily in direct contact with each other. + Rebecca Jackson + MI:2286 + functional association identification design + + + + + + + + + + + + + + + + + + + + + + + + + direct interaction identification design + + A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another. + Rebecca Jackson + molecular binding identification design + MI:0407 + direct interaction identification design + + + + + + + + + enzymatic reaction identification design + + A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme. + Rebecca Jackson + MI:0414 + enzymatic reaction identification design + + + + + + + + + self interaction identification design + + A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule. + Rebecca Jackson + MI:1126 + self interaction identification design + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + chromosome conformation capture sequencing assay + + A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. + Rebecca Jackson + 3C-seq assay + PMID:23411633 + https://github.com/obi-ontology/obi/issues/939 + chromosome conformation capture sequencing assay + + + + + + + + + inverse polymerase chain reaction + + A polymerase chain reaction which amplifies DNA with only one known sequence from which primers may be designed. A series of restriction digestions and ligations result in a looped DNA fragment which can be primed for PCR. + Rebecca Tauber + inverse PCR + url:https://en.wikipedia.org/wiki/Chromosome_conformation_capture + inverse polymerase chain reaction + + + + + + + + + + + + + + + swab specimen + + A specimen that is stored on a swab as the output of a collecting specimen with swab process. + Chris Stoeckert + OBIB/OBI + https://github.com/obi-ontology/obi/issues/910 + OBIB + swab specimen + + + + + + + + + collecting specimen with swab + + A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). + Chris Stoeckert + OBIB + https://github.com/obi-ontology/obi/issues/910 + OBIB + collecting specimen with swab + + + + + + + + + demultiplexed sequence data + + Sequence data in which an identifier subsequence has been used to categorize each reads by source. + Dan Berrios + Dan Berrios + demultiplexed sequence data + + + + + + + + + multiplexed sequence data + + Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source. + Dan Berrios + Dan Berrios + multiplexed sequence data + + + + + + + + + + + + + + + + + + + + + + + + + + + + + areolar swab specimen + + A specimen that is collected with a swab from the surface of an areola of a breast. + Chris Stoeckert + Chris Stoeckert, OBIB + areolar swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + breast swab specimen + + A specimen that is collected with a swab from the surface of a breast. + Chris Stoeckert + Chris Stoeckert, OBIB + breast swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cheek swab specimen + + A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. + Chris Stoeckert + Chris Stoeckert, OBIB + cheek swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nasopharyngeal swab specimen + + A specimen that is collected with a swab from the surface of a nasopharynx. + Chris Stoeckert + Chris Stoeckert, OBIB + nasopharyngeal swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oral swab specimen + + A specimen that is collected with a swab from the inside surface of a mouth. + Chris Stoeckert + Chris Stoeckert, OBIB + oral swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oropharyngeal swab specimen + + A specimen that is collected with a swab from the surface of a oropharynx. + Chris Stoeckert + Chris Stoeckert, OBIB + oropharyngeal swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + rectal swab specimen + + A specimen that is collected with a swab from the surface of a rectum. + Chris Stoeckert + Chris Stoeckert, OBIB + rectal swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tongue swab specimen + + A specimen that is collected with a swab from the surface of a tongue. + Chris Stoeckert + Chris Stoeckert, OBIB + tongue swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + vagina swab specimen + + A specimen that is collected with a swab from the surface of a vagina. + Chris Stoeckert + Chris Stoeckert, OBIB + vagina swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + fecal swab specimen + + A specimen that is collected with a swab from the surface of a feces. + Chris Stoeckert + stool swab specimen + Chris Stoeckert, OBIB + fecal swab specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + environmental swab specimen + + A specimen that is collected with a swab from the surface of an environmenal material. + Chris Stoeckert + Chris Stoeckert, OBIB + environmental swab specimen + + + + + + + + + birth cohort study design + The LucKi Birth Cohort Study was designed and started in 2006 to follow children from birth into adulthood on a wide range of determinants, disorders, and diseases. + + A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up. + MIABIS + MIABIS contributors + birth cohort study design + + + + + + + + + disease specific study design + A study of the symptoms experienced by patients who have been diagnosed with multiple sclerosis employs a disease specific study design. + + A study design for which material and information is collected from subjects that have already developed a particular disease. + MIABIS + MIABIS contributors + disease specific study design + + + + + + + + + genealogical record + A family tree is a type of genealogical record. + + A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption. + MIABIS + Sarah Bost + genealogical record + + + + + + + + + national registry + The Social Security Administration's Death Master File is a national registry in the United States. + + An information content entity that contains information about a nationwide group of individuals. + MIABIS + Sarah Bost + MIABIS contributors + national registry + + + + + + + + + national biomedical registry + The Care Register for Health Care, maintained by the Finnish National Institute for Health and Welfare, is a national biomedical registry. + + A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes. + MIABIS + Sarah Bost + MIABIS contributors + national biomedical registry + + + + + + + + + site-directed mutagenesis + Site-directed mutagenesis was used to prepare mutants of the Hypoxia-inducible factor-1 (HIF-1) alpha subunit to investigate the role of certain amino acids in hypoxia. (PMID:12393189) + + An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer. + Rebecca Jackson + url:https://www.ncbi.nlm.nih.gov/books/NBK21945/ + https://github.com/obi-ontology/obi/issues/1058 + site-directed mutagenesis + + + + + + + + + random mutagenesis + Error-prone PCR was used to introduce amino acid mutations to the cAMP receptor protein (CRP) of E. coli to investigate strain engineering to improve osmotolerance for industrial requirements. (PMID:22179860) + + An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR. + Rebecca Jackson + PMID:15153637 + https://github.com/obi-ontology/obi/issues/1058 + random mutagenesis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + reconstitution assay + "In an attempt to define the mechanism of insulin-regulated glucose transporter 4 (Glut4) translocation, we have developed an in vitro reconstitution assay... insulin-induced Glut4 translocation can be reconstituted in vitro to a limited extent by using isolated membranes." (PMID:10611313) + + An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. + Rebecca Jackson + reconstitution experiment + url:https://jcs.biologists.org/content/132/4/jcs227488 + https://github.com/obi-ontology/obi/issues/1059 + reconstitution assay + + + + + + + + + + + + + + + + + + + + in vitro transcription reconstitution assay + An in vitro reconstituted mouse transcription system helped identify an NF-Y interacting promoter as essential for high-level expression from the R2 promoter. (PMID:11502214) + + A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. + Rebecca Jackson + PMID:9237163 + https://github.com/obi-ontology/obi/issues/1059 + in vitro transcription reconstitution assay + + + + + + + + + whole metagenome sequencing assay + + A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. + Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). + Rebecca Jackson + WMS + Bjoern Peters + Michelle Giglio + https://github.com/obi-ontology/obi/issues/1056 + whole metagenome sequencing assay + + + + + + + + + case-control study design + + A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants. + John Judkins, Bjoern Peters + Wikipedia, OBI + case-control study design + + + + + + + + + gene knockdown + + A genetic transformation which reduces the expression of a specific gene or genes in an organism. + Rebecca Jackson + gene knock-down + url:https://en.wikipedia.org/wiki/Gene_knockdown + gene knockdown + + + + + + + + + + + + + + + RNAi gene knockdown + + A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease. + Rebecca Jackson + RNA interference gene knockdown + url:https://en.wikipedia.org/wiki/Gene_knockdown + RNAi gene knockdown + + + + + + + + + ribosomal RNA-depleted RNA extract + Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. + + An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). + Dan Berrios + https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 + ribosomal RNA-depleted RNA extract + + + + + + + + + + + + + + + RNAi knockdown assay + "Here, we described the development of RNAi by micro-injection of double-stranded RNA (dsRNA) in the pea aphid Acyrthosiphon pisum. Injection of dsRNA into whole aphid body induced the silencing of two marker genes with different expression patterns: the ubiquitously expressed Ap-crt genes encoding a calreticulin and the gut specific Ap-cath-L gene encoding a cathepsin-L." (PMID:17903251) + + A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. + Rebecca Jackson + RNA interference knockdown assay + RNAi gene knockdown assay + Rebecca Jackson + https://github.com/obi-ontology/obi/issues/1057 + RNAi knockdown assay + + + + + + + + + direct RNA sequencing assay + + An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. + Dan Berrios + DRS + direct RNA-seq + url:https://www.nature.com/articles/nature08390 + https://github.com/obi-ontology/obi/issues/874 + jahilton + direct RNA sequencing assay + + + + + + + + + + + + + + + Illumina NovaSeq 6000 + Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. + + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + Dan Berrios + NovaSeq 6000 + http://www.illumina.com/systems/sequencing-platforms/novaseq.html + Illumina NovaSeq 6000 + + + + + + + + + single-cell RNA sequencing assay + Single-cell RNA sequencing (scRNA-seq) assays provide the expression profiles of individual cells. + + An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin. + Dan Berrios + scRNA-seq + Anna Maria Masci + single-cell RNA sequencing assay + + + + + + + + + PacBio Sequel + The cDNAs were sequenced on the PacBio Sequel platform. + + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + Bonita Lam + Dan Berrios + Pacific BioSciences Sequel + http://www.pacb.com/products-and-services/pacbio-systems/sequel/ + PacBio Sequel + + + + + + + + + PacBio Sequel II + The cDNAs were sequenced on the PacBio Sequel II platform. + + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. + Bonita Lam + Dan Berrios + Pacific BioSciences Sequel II + http://www.pacb.com/products-and-services/pacbio-systems/sequel/ + PacBio Sequel II + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells + + An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + disease exacerbation after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells + + An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + decreased disease after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells + + An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + decreased disease after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells + + An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + protection from challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells + + An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden + + An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. + IEDB + IEDB + pathogen burden after challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden + + An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. + IEDB + IEDB + pathogen burden after challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival. + IEDB + IEDB + survival from other challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. + IEDB + IEDB + survival from other challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden + + An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden. + IEDB + IEDB + tumor burden after challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden + + An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden. + IEDB + IEDB + tumor burden after challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells + + An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + tolerance after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells + + An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + tolerance after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Giemsa stain assay + Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs + + An assay that uses a Giemsa stain to characterize cells. + Chris Stoeckert + Jie Zheng + https://github.com/obi-ontology/obi/issues/1093 + VEuPathDB + Giemsa stain assay - + - - - pipette - A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. - Stephen A. Fisher, Junhyong Kim, Dan Berrios - https://en.wikipedia.org/wiki/Pipette - pipette + + + + + + 1 + + + + individual organism specimen + + A specimen composed of an individual organism to be studied in an investigation. + Person: Jie Zheng + EFO_0000542 individual + https://github.com/obi-ontology/obi/issues/1092 + individual organism specimen - + - + @@ -62186,7 +78769,7 @@ https://www.doi.org/ - + @@ -62197,7 +78780,7 @@ https://www.doi.org/ - + @@ -62209,10 +78792,34 @@ https://www.doi.org/ + + + + + + + + + + + + + + + + + + + + + + + + - + @@ -62221,2455 +78828,2973 @@ https://www.doi.org/ + + + + + + + + + + + - an organism identification assay that uses a differential medium to achieve its objective - John Judkins - bacteriological assay - EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm - differential medium assay - - - - - - - - - A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material - John Judkins - medication timepoint - OBI - VEuPathDB - medication time value specification - - - - - - - - - A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment - John Judkins - medication dose - OBI - VEuPathDB - medication dose value specification - - - - - - - - - A role that is borne by a case-control study design participant under investigation that is associated with the outcome mentioned in the study design. - John Judkins, Bjoern Peters - OBI - case role in case-control study - - - - - - - - - A role that is borne by a case-control study design participant under investigation that is not associated with the outcome mentioned in the study design. - John Judkins, Bjoern Peters - OBI - control role in case-control study + blood microbiology assay + + An organism identification assay that identifies a microorganism in a blood specimen. + John Judkins + https://github.com/obi-ontology/obi/issues/1064 + blood microbiology assay - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + biopsy + Biopsy of a potentially cancerous mole. - A specimen that is derived from amniotic fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - amniotic fluid specimen + A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. + Damion Dooley + Nicole Vasilevsky + https://en.wikipedia.org/wiki/Biopsy + biopsy - + - - - - - - - - - - - - - - - - - - - - + + + image guided biopsy + Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland. - A specimen that is derived from bile. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - bile specimen + A biopsy which uses an imaging procedure to guide a needle biopsy. + Damion Dooley + image guided needle biopsy + image-guided biopsy + imaging guided biopsy + https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 + image guided biopsy - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + computed tomography assisted biopsy + A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle. - A specimen that is derived from cerbrospinal fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - cerebrospinal fluid specimen + A needle biopsy guided by real-time computed tomography (CT) scan images. + Damion Dooley + CT Assisted Biopsy + CT Guided Biopsy + Computed Tomography Assisted Biopsy + Computed Tomography-Guided Needle Biopsy + http://purl.obolibrary.org/obo/NCIT_C137909 + computed tomography assisted biopsy - + - - - - - - - - - - - - - - - - - - - - + + + ultrasound-guided needle biopsy + An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid. - A specimen that is derived from feces. - Chris Stoeckert - stool specimen - Chris Stoeckert, Penn Medicine Biobank - feces specimen + A needle biopsy guided by ultrasound visualization. + Damion Dooley + https://www.oncolink.org/cancer-treatment/procedures-diagnostic-tests/biopsy-procedures/ultrasound-guided-needle-biopsy + ultrasound-guided needle biopsy - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + needle biopsy + A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin. - A specimen that is derived from digestive system fluid or secretion. - Chris Stoeckert - gastric fluid specimen - Chris Stoeckert, Penn Medicine Biobank - digestive system fluid or secretion specimen + A biopsy that uses a hollow needle to extract cells. + Damion Dooley + https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749 + needle biopsy - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from milk. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - milk specimen + + + fine needle aspiration biopsy + A fine needle aspiration biopsy is commonly performed in order to test for cancer. + + A biopsy that uses a thin needle to extract cells. + Chris Stoeckert, Helena Ellis, Jie Zheng + FNA + FNAB + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ + NCI BBRB + fine needle aspiration biopsy - + - - - - - - - - - - - - - - - - - - - - + + + core needle biopsy + A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed. - A specimen that is derived from pericardial fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - pericardial fluid specimen + A biopsy that uses a hollow tube to collect a core of tissue. + Chris Stoeckert, Helena Ellis, Jie Zheng + CNB + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ + NCI BBRB + core needle biopsy - + - - - - - - - - - - - - - - - - - - - - + + + surgical biopsy + Surgical biopsy may be required to collect hard-to-reach tissue. - A specimen that is derived from saliva. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - saliva specimen + A biopsy involving a surgical incision into an organism to access the biopsy material. + Damion Dooley + excisional biopsy + open biopsy + https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 + surgical biopsy - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + abdominal wall fat pad biopsy + The makeup of fat in the abdominal wall can be investigated by fat biopsy. - A specimen that is derived from sputum. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - sputum specimen + A biopsy involving the collection of a small part of the abdominal wall fat pad. + Nicole Vasilevsky, Damion Dooley + abdominal wall biopsy + fat biopsy + https://www.ucsfbenioffchildrens.org/tests/003841.html + abdominal wall fat pad biopsy - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + tail biopsy + A mouse tail biopsy was performed to collect material for DNA extraction. - A specimen that is derived from sweat. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - sweat specimen + A biopsy involving the collection of the tip of a mamallian tail. + Nicole Vasilevsky, Damion Dooley + snip + http://web.jhu.edu/animalcare/policies/Tail%20Biopsy%20of%20Mice.pdf + tail biopsy - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + bone marrow biopsy + A bone marrow biopsy removes bone with the marrow inside to look at under a microscope - A specimen that is derived from synovial fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - synovial fluid specimen + A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected. + Nicole Vasilevsky + http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy + bone marrow biopsy - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + skinpunch biopsy + A three or four millimeter punch is used in s skinpunch biopsy proceedure. - A specimen that is derived from vireous humor. - Chris Stoeckert - vitreous fluid specimen - Chris Stoeckert, Penn Medicine Biobank - vitreous humor specimen + A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool. + Nicole Vasilevsky + punch biopsy; skin biopsy + http://healthlibrary.epnet.com/GetContent.aspx?token=b93d114e-5009-4f6a-9917-6c594254fcc7&chunkiid=14861 + skinpunch biopsy - + - + - - - - - - - + + + + - - + + + + + + + + + + + + - - + + - - A specimen that is derived from bone marrow. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - bone marrow specimen + cytometric bead array assay measuring epitope specific interleukin-15 production by T cells + + A cytometric bead array assay that detects interleukin-15 production by T cells. + IEDB + IEDB + IL-15 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-15 production by T cells - + - + - - - - - - - + + + + - - + + + + + + + + + + + + - - + + - - A specimen that is derived from placenta. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - placenta specimen + cytometric bead array assay measuring epitope specific interleukin-16 production by T cells + + A cytometric bead array assay that detects interleukin-16 production by T cells. + IEDB + IEDB + IL-16 release|cytometric bead array + cytometric bead array assay measuring epitope specific interleukin-16 production by T cells - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + - - A specimen that is derived from peritoneal fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - peritoneal fluid specimen + in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells + + An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + hypersensitivity after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + - - A specimen that is derived from pleural fluid. - Chris Stoeckert - Chris Stoeckert, Penn Medicine Biobank - pleural fluid specimen + in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells + + An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + type IV hypersensitivity (DTH) after adoptive transfer|in vivo skin test + in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + - - A specimen that is derived from brain. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - brain specimen + in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells + + A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + proliferation after adoptive transfer|in vivo assay + in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + - - A specimen that is derived from hair. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - hair specimen + assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells + + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + antibody help after adoptive transfer|in vivo assay + assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + - - A specimen that is derived from prostate gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - prostate gland specimen + assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells + + A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + T cell help after adoptive transfer|in vivo assay + assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + - - A specimen that is derived from skeletal muscle. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - skeletal muscle tissue specimen + in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells + + An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells. + IEDB + IEDB + cytotoxicity after adoptive transfer|in vivo assay + in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells - + - + - - - - - - - + + + + - - + + + + + + + + + + + + - - + + - - A specimen that is derived from heart. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - heart specimen + ELISA measuring epitope specific perforin release by T cells + + An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells. + IEDB + IEDB + perforin release|ELISA + ELISA measuring epitope specific perforin release by T cells - + - - - - - - - - - - - - - - - - - - - - + + + enrichment culture medium + Selenite broth is an enrichment culture medium used to selectively isolate Salmonella species. - A specimen that is derived from renal medulla. - Chris Stoeckert - kidney medulla specimen - Chris Stoeckert, NCI BBRB - renal medulla specimen + A culture medium that is designed to favor the growth of a particular microorganism or cells over others, enriching a sample for the microorganism or cells of interest. + + + isolation medium + + 2020-03-08T22:04:07Z + enrichment culture medium + - + - - - - - - - - - - - - - - - - - - - - + + + case series study design + PMID: 22213493 - A specimen that is derived from adrenal gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - adrenal gland specimen + A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included. + http://orcid.org/0000-0002-8844-9165 + https://www.ncbi.nlm.nih.gov/pubmed/22213493 + case series design - + - - - - - - - - - - - - - - - - - - - - + + + massively parallel reporter assay - A specimen that is derived from breast. - Chris Stoeckert - mammary tissue specimen - Chris Stoeckert, NCI BBRB - breast specimen + An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. + Damion Dooley + MPRA + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364389/ + massively parallel reporter assay - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + - - + + - - A specimen that is derived from urinary bladder. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - urinary bladder specimen + in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells + + An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + in vivo response after adoptive transfer|in vivo assay + in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + - - + + - - A specimen that is derived from tibial artery. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - tibial artery specimen + in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells + + An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + in vivo response after adoptive transfer|in vivo assay + in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells - + - + - - - + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + - - + + - - A specimen that is derived from skin. - Chris Stoeckert - skin specimen - Chris Stoeckert, NCI BBRB - skin of body specimen + in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells + + An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specfic T cells. + IEDB + IEDB + disease exacerbation after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from pancreas. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - pancreas specimen + + + + + + + + + vacuum-assisted biopsy needle + Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source. + + A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material. + Damion Dooley + https://www.researchgate.net/publication/330227873 + https://github.com/obi-ontology/obi/issues/1163 + vacuum-assisted biopsy needle - + - - - - - - - - - - - - - - - - - - - - + + + pseudovirus entry assay + “Inhibition of MERS-CoV-spike-mediated pseudovirus entry by the HKU4 S1 domain “ (from https://doi.org/10.1073/pnas.1405889111); “protease treatment did not enhance pseudotype entry in the absence of host receptor “; “bat-derived cell lines derived from other species were infected with VSV-reporter particles pseudotyped with chimeric spikes and luciferase was measured as readout for cell entry” (from https://doi.org/10.1038/s41564-020-0688-y) ; “teicoplanin could inhibit the entry of HIV-1-2019-nCoV-S pseudoviruses with the IC50 value of 1.66 uM” (from https://doi.org/10.1101/2020.02.05.935387) - A specimen that is derived from stomach. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - stomach specimen + An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. + Thomas Lemberger + pseudotype cell entry + pseudotype entry + pseudotyped particle cell entry assay + pseudovirus cell entry + Figure 1c in https://doi.org/10.1038/s41564-020-0688-y or Materials & Method in https://www.pnas.org/content/111/34/12516 + pseudovirus entry assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from pituitary gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - pituitary gland specimen + + + + + + + + + glass bottle + + A container with a narrow neck that is made of glass. + VEuPathDB + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + glass bottle - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from adipose tissue. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - adipose tissue specimen + + + + + + + + + glass bottle coated with insecticides + + A glass bottle that coated with material designed to control insects. + VEuPathDB + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + glass bottle coated with insecticides - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from cortex of kidney. - Chris Stoeckert - kidney cortex specimen - Chris Stoeckert, NCI BBRB - cortex of kidney specimen + + + short interspersed nuclear elements polymerase chain reaction + + A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). + Jie Zheng + short interspersed elements PCR + PMID: 12711348 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + short interspersed nuclear elements polymerase chain reaction - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from esophagus mucosa. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - esophagus mucosa specimen + + + nested polymerase chain reaction + + A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction. + Jie Zheng + nested-PCR + nested PCR + https://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + nested polymerase chain reaction - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from colon. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - colon specimen + + + immunoelectrophoresis + + An electrophoresis that separates and characterize proteins based on reaction with antibodies. + Jie Zheng + IEP + https://en.wikipedia.org/wiki/Immunoelectrophoresis + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + immunoelectrophoresis - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from lung. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - lung specimen + + + counter current immunoelectrophoresis + + An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions. + Jie Zheng + http://www.ispybio.com/search/protocols/ie%20protocol2.pdf + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + counter current immunoelectrophoresis - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from esophagus muscularis mucosa. - Chris Stoeckert - esophagus muscularis specimen - Chris Stoeckert, NCI BBRB - esophagus muscularis mucosa specimen + + + ligase detection reaction + + A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product. + Jie Zheng + LDR + MIRO:20000103 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + ligase detection reaction - + - + + + loop-mediated isothermal amplification + + An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR. + Jie Zheng + LAMP + https://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + loop-mediated isothermal amplification + + + + + + + + + detection of pathogenic organisms objective + + An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + detection of pathogenic organisms objective + + + + + + + + + insecticide resistance detection objective + + An organism feature identification objective that aims to detect insecticide resistance of an insect. + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance detection objective + + + + + + + + + arthropod meal of blood specimen + A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. + + A specimen of the blood ingested by an arthropod. + The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. + Chris Stoeckert + Jie Zheng + blood meal + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + arthropod meal of blood specimen + + + + + + + - - - - - - - - - - - - - + + + + + - - A specimen that is derived from cerebral cortex. - Chris Stoeckert - brain cortex specimen - Chris Stoeckert, NCI BBRB - cerebral cortex specimen + polymerase chain reaction assay + + An assay that uses polymerase chain reaction technique to amplify DNA. + VEuPathDB + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + polymerase chain reaction assay - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - - A specimen that is derived from thyroid gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - thyroid gland specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + restriction fragment length polymorphism assay + + An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. + VEuPathDB + RFLP + restriction fragment length polymorphism + restriction fragment length polymorphism analysis + https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + restriction fragment length polymorphism assay - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - A specimen that is derived from cerebellum. - Chris Stoeckert - brain cerebellum specimen - Chris Stoeckert, NCI BBRB - cerebellum specimen + + DNA fingerprinting assay + + An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. + VEuPathDB + DNA finger printing + DNA fingerprint + DNA fingerprinting + DNA profiling + VEuPathDB + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + DNA fingerprinting assay - + - + - - - - - - - - - - - - - + + + + + - - A specimen that is derived from tibial nerve. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - tibial nerve specimen + insecticide resistance assay + + An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. + VEuPathDB + resistance identification/monitoring + MIRO:20000001 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from coronary artery. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - coronary artery specimen + + + + + + + + + insecticide resistance by monitoring known mutations assay + + An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. + VEuPathDB + monitoring known mutations + MIRO:20000096 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by monitoring known mutations assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from spleen. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - spleen specimen + + + + + + + + + + + + + + + + + + + + insecticide resistance by detecting enzyme activity assay + + An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. + VEuPathDB + metabolic resistance assay + MIRO:20000003 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by detecting enzyme activity assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from aorta. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - aorta specimen + + + + + + + + + insecticide resistance bioassay + + An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. + VEuPathDB + bioassay + MIRO:20000058 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance bioassay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from the atrium auricular region. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - atrial appendage specimen + + + + + + + + + + + + + + + + + + + + insecticide resistance by detecting alpha esterase activity assay + + An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. + VEuPathDB + alpha esterase activity assay + IRO:0000149 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by detecting alpha esterase activity assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from the esophagogastric junction. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - esophagogastric junction specimen + + + + + + + + + + + + + + + + + + + + insecticide resistance by detecting beta esterase activity assay + + An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. + VEuPathDB + beta esterase activity assay + IRO:0000150 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by detecting beta esterase activity assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from ileum. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - ileum specimen + + + + + + + + + + + + + + + + + + + + insecticide resistance by detecting acetylcholinesterase activity assay + + An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. + VEuPathDB + AChE activity assay + AChE assay + acetylcholinesterase assay + MIRO:20000010 + MIRO:20000084 + MIRO:20000086 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by detecting acetylcholinesterase activity assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from liver. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - liver specimen + + + + + + + + + + + + + + + + + + + + insecticide resistance by detecting glutathione S-transferase activity assay + + An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). + VEuPathDB + GST related assay + MIRO:20000083 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by detecting glutathione S-transferase activity assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from minor salivary gland. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - minor salivary gland specimen + + + + + + + + + + + + + + + + + + + + insecticide resistance by detecting carboxylic ester hydrolase activity assay + + An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. + VEuPathDB + pNPA assay + MIRO:20000019 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by detecting carboxylic ester hydrolase activity assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from omentum. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - omentum specimen + + + + + + + + + insecticide resistance by detecting mixed-function oxidase assay + + An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. + VEuPathDB + mixed-function oxidase assay + MIRO:20000062 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by detecting mixed-function oxidase assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from female gonad. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - ovary specimen + + + + + + + + + direct insecticide resistance bioassay + + An insecticide resistance bioassay without the use of any synergist. + VEuPathDB + direct bioassay + MIRO:20000044 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + direct insecticide resistance bioassay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from sigmoid colon. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - sigmoid colon specimen + + + + + + + + + topical application insecticide resistance bioassay + + An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. + VEuPathDB + topical application assay + IRO:0000155 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + topical application insecticide resistance bioassay - + - - + + + + + + + + + direct insecticide resistance diagnostic assay + + A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. + VEuPathDB + diagnostic test + MIRO:20000075 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + direct insecticide resistance diagnostic assay + + + + + + + + + + + + + + + insecticide resistance dose response assay + + A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. + VEuPathDB + dose response test + MIRO:20000076 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance dose response assay + + + + + + + + + + + + + + + insecticide resistance time response assay + + A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. + VEuPathDB + time response test + MIRO:20000013 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance time response assay + + + + + + + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - - A specimen that is derived from suprapubic skin. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - suprapubic skin specimen + + + + + + + + Centre for Disease Control and Prevention bottle bioassay + + A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. + VEuPathDB + CDC bottle bioassay + MIRO:20000009 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + Centre for Disease Control and Prevention bottle bioassay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from testis. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - testis specimen + + + + + + + + + WHO cone kit diagnostic assay + + A direct insecticide resistance diagnostic assay uses WHO cone kit. + VEuPathDB + cone DT + MIRO:20000039 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + WHO cone kit diagnostic assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from uterus. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - uterus specimen + + + + + + + + + WHO paper kit diagnostic assay + + A direct insecticide resistance diagnostic assay uses WHO paper kit. + VEuPathDB + WHO paper kit DT + MIRO:20000041 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + WHO paper kit diagnostic assay - + - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from vagina. - Chris Stoeckert - Chris Stoeckert, NCI BBRB - vagina specimen + + + + + + + + + WHO larvicide diagnostic assay + + A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. + VEuPathDB + WHO larvicide DT + MIRO:20000049 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + WHO larvicide diagnostic assay - + - - + + - - + + + + + + + + + + + + - - + + - "18-33 years old" - An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. - Mathias Brochhausen - #839 - age group inclusion criterion - - - - - - - - - A value specifcation that specifies the youngest age when specifying an age range. - Mathias Brochhausen - minimum age value specification + + + + + + + insecticide resistance dose response by bottle assay + + An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. + VEuPathDB + bottle bioassay DR test + MIRO:20000011 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance dose response by bottle assay - + - - - A value specifcation that specifies the oldest age when specifying an age range. - Mathias Brochhausen - maximum age value specification + + + + + + + + + insecticide resistance dose response by survival of larvae assay + + An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. + VEuPathDB + WHO larvicide DR test + MIRO:20000050 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance dose response by survival of larvae assay - + - - - "received at least 2 days of vancomycin" - An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process. - Mathias Brochhausen - #840 - use of medication inclusion criterion + + + + + + + + + insecticide resistance dose response by WHO paper kit assay + + An insecticide resistance dose response assay using WHO paper kit. + VEuPathDB + WHO paper kit DR test + MIRO:20000048 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance dose response by WHO paper kit assay - + - - - "included hospital patients" - An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process. - Mathias Brochhausen - hospital patient inclusion criterion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + insecticide resistance time response by bottle assay + + An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. + VEuPathDB + bottle bioassay TR test + MIRO:20000030 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance time response by bottle assay - + - - - "included married and unmarried patients", "included divorced individuals" - An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process. - Mathias Brochhausen - family status inclusion criterion + + + + + + + + + insecticide resistance time response by WHO paper kit assay + + An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. + VEuPathDB + WHO paper kit TR test + MIRO:20000036 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance time response by WHO paper kit assay - + - - - "included males and females", "included male patients" - An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process. - Mathias Brochhausen - sex inclusion criterion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + insecticide resistance by amplification refractory mutation system assay + + An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations. + VEuPathDB + ARMS + Amplification Refractory Mutation System + IRO:0000006 + PMID: 18428319 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by amplification refractory mutation system assay - + - - - "include US residents" - An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process. - Mathias Brochhausen - country of residence inclusion criteria + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + insecticide resistance by primer introduced restriction analysis PCR assay + + An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. + VEuPathDB + PIRA-PCR + Primer Introduced Restriction Analysis PCR + polymerase chain reaction-primer-introduced restriction analysis + IRO:0000007 + PMID: 8339229 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by primer introduced restriction analysis PCR assay - + - - - "include only Hispanic individuals" - An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process. - Mathias Brochhausen - ethnicity inclusion criterion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + insecticide resistance by nested polymerase chain reaction assay + + An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. + VEuPathDB + gene mutation detection by nested PCR + IRO:0000127 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by nested polymerase chain reaction assay - + - - - A histological assay that is intended to check for the presence or level of a specific disease. - OBI - histopathology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + insecticide resistance by ligase detection reaction assay + + An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. + VEuPathDB + MIRO:20000103 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by ligase detection reaction assay - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). - Dan Berrios - Dan Berrios - adapter-sequence trimming - - - - - - - - - A data transformation in which data contained in 2 or more files are merged into a single file. - Dan Berrios - Dan Berrios - file merge + insecticide resistance by ligase detection reaction-fluorescent microsphere assay + + An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. + VEuPathDB + gene mutation detection by LDR-FMA + ligase detection reaction-fluorescent microsphere assay + IRO:0000151 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by ligase detection reaction-fluorescent microsphere assay - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. - Dan Berrios - Dan Berrios - sequence alignment + insecticide resistance by PCR amplification of specific alleles assay + + An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. + VEuPathDB + PASA + PCR amplification of specific alleles + allele-specific amplification and amplification refractory mutation system + PMID: 1734929 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by PCR amplification of specific alleles assay - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables. - Dan Berrios - Dan Berrios - sequence data feature count tabulation + insecticide resistance by fluorogenic PCR assay + + An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. + VEuPathDB + MIRO:20000102 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by fluorogenic PCR assay - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective. - Dan Berrios - Dan Berrios - trimmed sequence data - - - - - - - - + - - + + - Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 - - A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 - https://www.nanostring.com/products/mirna-assays/mirna-panels - nCounter Mouse miRNA Expression array - - - - - - - - - - + + + + + + + + + - An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. - Jason Hilton - Mark A. Miller - mRNA-seq - url:https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-419 - ENCODE - polyA-selected RNA sequencing assay - - - - - - - - - - + + - An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. - Jason Hilton - Mark A. Miller - polyA-depleted RNA-seq - url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030733 - url:http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1110676 - ENCODE - polyA-depleted RNA sequencing assay + insecticide resistance by PCR-RFLP assay + + An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. + VEuPathDB + PCR-RFLP + MIRO:20000113 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by PCR-RFLP assay - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - polyA depleted RNA extract - A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. - Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 - PERSON: Chris Stoeckert - PERSON: Jie Zheng - UPenn Group - 2018-05-11T16:35:11Z - polyA depleted RNA extract - - - - - - - - - RNA extraction with polyA depletion - A RNA extraction process in which only RNAs lacking a polyA tail are retained - Mark A. Miller, based on OBI_0000848 - UPenn Group - 2018-05-11T15:01:14Z - RNA extraction with polyA depletion - - - - - - - - - Novel transcript forms were assessed by isoform sequencing. - A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. - ISO-seq - url:http://www.pacb.com/blog/intro-to-iso-seq-method-full-leng/ - isoform sequencing - - - - - - - - - Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run. - Dan Berrios - Dan Berrios - adapter sequence data - - - - - - - - - The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. - Dan Berrios - Dan Berrios - adapter-trimmed sequence data - - - - - - - - - The results of a sequence alignment. - Dan Berrios - Dan Berrios - aligned sequence data - - - - - - - - - - + + - The results of a data transformation of sequence data in which files containing aligned sequence data are merged together - Dan Berrios - Dan Berrios - merged aligned sequence data + insecticide resistance by short interspersed elements PCR assay + + An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). + VEuPathDB + Short Interspersed Elements PCR + IRO:0000013 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + insecticide resistance by short interspersed elements PCR assay - + - - - The results of a sequence data feature count tabulation. - Dan Berrios - Dan Berrios - sequence library feature count data + + + + + + + + + + + + + + + + + + + + + + pathogen detection assay + + An organism identification assay that aims to detect pathogens. + VEuPathDB + pathogen detection method + IRO:0000137 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + pathogen detection assay - + - - + + - - + + + + + + + - The results of a DNA methylation profiling assay - DNA methylation profiling data - - - - - - - - - The results of a differential expression analysis. - differential expression analysis data - - - - - - - - - A data transformation in which subsequences of a molecular sequence are cut (removed). - sequence trimming - - - - - - - - - - + + - digital acquisition card - The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device). - Mark A. Miller - DAQ device - digital acquisition and digital generation card - Brenda Farrell, bfarrell@bcm.edu - digital acquisition card - - - - - - - - - machine learning - A planned process in which statistical techniques are used to give computers the ability to learn about patterns in data, without being explicitly programmed. Learning is defined in this case as progressively improving performance on a specific task. - Mark A. Miller - https://en.wikipedia.org/wiki/Machine_learning - https://github.com/TrisSN - machine learning - - - - - - - - - supervised machine learning - A machine learning process using a function that maps an input to an output based on example input-output pairs. It infers a function from labeled training data consisting of a set of training examples. - Mark A. Miller - https://en.wikipedia.org/wiki/Supervised_learning - https://github.com/TrisSN - supervised machine learning - - - - - - - - - unsupervised machine learning - A machine learning process that infers a function describing the structure of "unlabeled" data (i.e. data that has not been classified or categorized). - Mark A. Miller - https://en.wikipedia.org/wiki/Unsupervised_learning - https://github.com/TrisSN - unsupervised machine learning + VectorTest assay + + A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. + VEuPathDB + VectorTest + IRO:0000138 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + VectorTest assay - + - - + + - - + + + + + + + - A study design that investigates the features of interaction between molecules. - Rebecca Jackson - person:RCT - molecular interaction identification design - - - - - - - - - A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules. - Rebecca Jackson - url:https://en.wikipedia.org/wiki/Colocalization - colocalization identification design + + + + + + + pathogen detection by Rapid Analyte Measurement Platform assay + + A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. + VEuPathDB + Rapid Analyte Measurement Platform + IRO:0000164 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + pathogen detection by Rapid Analyte Measurement Platform assay - + - - + + - - - - - - - - - - - + - A molecular interaction identification design that investigates a phenotype that is the result of two or more genetic perturbations, and is not explained by the individual genetic perturbations alone. - Rebecca Jackson - MI:0208 - genetic interaction identification design - - - - - - - - - A molecular interaction identification design that investigates a relationship that is the result of intermediate steps between two or more molecules that are not necessarily in direct contact with each other. - Rebecca Jackson - MI:2286 - functional association identification design - - - - - - - - - + - - - - - - - + + - A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another. - Rebecca Jackson - molecular binding identification design - MI:0407 - direct interaction identification design + + + + + + + pathogen detection by loop-mediated isothermal amplification assay + + A pathogen detection assay that is based on loop-mediated isothermal amplification. + VEuPathDB + Loop-mediated isothermal amplification + IRO:0000165 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + pathogen detection by loop-mediated isothermal amplification assay - + - - - A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme. - Rebecca Jackson - MI:0414 - enzymatic reaction identification design + + + + + + + + + + + + + blood meal assay + + An assay that analyzes the specimen taken from blood meal fed organism, such as insect. + VEuPathDB + blood meal analysis + IRO:0000135 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + blood meal assay - + - - - A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule. - Rebecca Jackson - MI:1126 - self interaction identification design + + + + + + + + + + + + + + + blood meal by counter current immunoelectrophoresis assay + + A blood meal assay that uses a counter current immunoelectrophoresis technique. + VEuPathDB + CIE + countercurrent immunoelectrophoresis + IRO:0000136 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + blood meal by counter current immunoelectrophoresis assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -64681,7 +81806,7 @@ https://www.doi.org/ - + @@ -64692,7 +81817,7 @@ https://www.doi.org/ - + @@ -64706,972 +81831,998 @@ https://www.doi.org/ - - + + + DNA based blood meal finger printing assay + + A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. + VEuPathDB + DNA based blood meal finger printing + VEuPathDB + VSMO:0001307 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + DNA based blood meal finger printing assay + + + + + + + + - - - - - - - + + - A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. - Rebecca Jackson - 3C-seq assay - PMID:23411633 - https://github.com/obi-ontology/obi/issues/939 - chromosome conformation capture sequencing assay + organism identification by size assay + + An organism identification assay that is based on the size of organism. + VEuPathDB + by size + IRO:0000145 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + organism identification by size assay - + - - - A polymerase chain reaction which amplifies DNA with only one known sequence from which primers may be designed. A series of restriction digestions and ligations result in a looped DNA fragment which can be primed for PCR. - Rebecca Tauber - inverse PCR - url:https://en.wikipedia.org/wiki/Chromosome_conformation_capture - inverse polymerase chain reaction + + + + + + + + + organism identification by cross mating assay + + An organism identification assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. + VEuPathDB + cross mating experiment + MIRO:30000036 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + organism identification by cross mating assay - + - - + + + - - + + - - - swab specimen - - A specimen that is stored on a swab as the output of a collecting specimen with swab process. - Chris Stoeckert - OBIB/OBI - https://github.com/obi-ontology/obi/issues/910 - OBIB - swab specimen + + organism identification by cytological chromosome examination assay + + An organism identification assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. + VEuPathDB + cytological chromosome examination + MIRO:30000037 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + organism identification by cytological chromosome examination assay - + - - - collecting specimen with swab - - A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). - Chris Stoeckert - OBIB - https://github.com/obi-ontology/obi/issues/910 - OBIB - collecting specimen with swab + + + + + + + + + + + + + + + organism identification by isoenzyme electrophoresis assay + + An organism identification assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. + VEuPathDB + isoenzyme electrophoresis + MIRO:30000038 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + organism identification by isoenzyme electrophoresis assay - + - - - Sequence data in which an identifier subsequence has been used to categorize each reads by source. - Dan Berrios - Dan Berrios - demultiplexed sequence data + + + + + + + + + organism identification by morphological examination assay + + An organism identification assay that is based on examination of morphology and the use of specific "taxonomic keys" to determine the species of the specimen. + VEuPathDB + morphological examination + MIRO:30000039 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + organism identification by morphological examination assay - + - - - Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source. - Dan Berrios - Dan Berrios - multiplexed sequence data + + + + + + + + + + + + + + + organism identification by PCR assay + + An organism identification assay that is based on PCR. + VEuPathDB + PCR-based species identification + MIRO:30000040 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + organism identification by PCR assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is collected with a swab from the surface of an areola of a breast. - Chris Stoeckert - Chris Stoeckert, OBIB - areolar swab specimen + + + + + + + + + + + + + + + organism identification by specific DNA hybridization assay + + An organism identification assay that is based on DNA hybrdization. + VEuPathDB + species specific DNA hybridization + MIRO:30000041 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + organism identification by specific DNA hybridization assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is collected with a swab from the surface of a breast. - Chris Stoeckert - Chris Stoeckert, OBIB - breast swab specimen + + + + + + + + + organism identification by salinity tolerance assay + + An organism identification assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. + VEuPathDB + salinity tolerance tests + MIRO:30000042 + https://github.com/obi-ontology/obi/issues/1117 + VEuPathDB + organism identification by salinity tolerance assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. - Chris Stoeckert - Chris Stoeckert, OBIB - cheek swab specimen + + + molecular label role + + A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. + MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role). +JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced REO_0000171 by newly assigned ID: OBI:0002743. + Group: OBI + molecular tracer role + OBI developer call, 3-12-12 + https://github.com/obi-ontology/obi/issues/1135 + molecular label role - + - + - - - - - - - - - - - - - - - - - - - + + + + + - - A specimen that is collected with a swab from the surface of a nasopharynx. - Chris Stoeckert - Chris Stoeckert, OBIB - nasopharyngeal swab specimen + + molecular label + + A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay + JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744. + Group: OBI + molecular tracer + OBI developer call, 3-12-12 + https://github.com/obi-ontology/obi/issues/1135 + molecular label - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + vacuum-assisted biopsy + A vacuum assisted biopsy can remove an area of abnormal cells from breast tissue. - A specimen that is collected with a swab from the inside surface of a mouth. - Chris Stoeckert - Chris Stoeckert, OBIB - oral swab specimen + A biopsy performed with a needle augmented with a vacuum device. + Damion Dooley + VAB + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ + vacuum-assisted biopsy - + - - + + - - - - - - - - - - - - - - - - - - - + + + + + + + + + - - - A specimen that is collected with a swab from the surface of a oropharynx. - Chris Stoeckert - Chris Stoeckert, OBIB - oropharyngeal swab specimen + + induced sputum specimen + + A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. + John Judkins + PMC3297553 + induced sputum specimen - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is collected with a swab from the surface of a rectum. - Chris Stoeckert - Chris Stoeckert, OBIB - rectal swab specimen + + + passage process + + A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. + John Judkins + https://en.wikipedia.org/wiki/Serial_passage + https://www.merriam-webster.com/dictionary/passage + passage process - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is collected with a swab from the surface of a tongue. - Chris Stoeckert - Chris Stoeckert, OBIB - tongue swab specimen + + + + + + + + + passage history record + + A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process. + John Judkins + https://en.wikipedia.org/wiki/Serial_passage + https://www.merriam-webster.com/dictionary/passage + passage history record - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is collected with a swab from the surface of a vagina. - Chris Stoeckert - Chris Stoeckert, OBIB - vagina swab specimen + + + + + + + + + + + Oxford Nanopore MinION + Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION + + A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + PERSON: Bonita Lam + ONT MinION, MinION + https://nanoporetech.com/products/minion + Oxford Nanopore MinION - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is collected with a swab from the surface of a feces. - Chris Stoeckert - stool swab specimen - Chris Stoeckert, OBIB - fecal swab specimen + + + + + + + + + Oxford Nanopore GridION Mk1 + Nineteen libraries were constructed and sequenced on nineteen different R9.4 FlowCells using the GridION X5 sequencer + + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually. + PERSON: Bonita Lam + Oxford Nanopore GridION X5, GridION Mk1 + https://nanoporetech.com/products/gridion + Oxford Nanopore GridION Mk1 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is collected with a swab from the surface of an environmenal material. - Chris Stoeckert - Chris Stoeckert, OBIB - environmental swab specimen + + + + + + + + + Oxford Nanopore PromethION + Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. + + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + PERSON: Bonita Lam + PromethION + https://nanoporetech.com/products/promethion + Oxford Nanopore PromethION - + - - - The LucKi Birth Cohort Study was designed and started in 2006 to follow children from birth into adulthood on a wide range of determinants, disorders, and diseases. - A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up. - MIABIS - MIABIS contributors - birth cohort study design + + + + + + + + + PRO-cap + + Precision nuclear run-on and sequencing to detect Pol II initiation sites + Bonita Lam + PRO-CAP + https://github.com/obi-ontology/obi/issues/1102 + PRO-cap - + - - - A study of the symptoms experienced by patients who have been diagnosed with multiple sclerosis employs a disease specific study design. - A study design for which material and information is collected from subjects that have already developed a particular disease. - MIABIS - MIABIS contributors - disease specific study design + + + + cDNA library + cDNA library lacks the non-coding and regulatory elements found in genomic DNA + + A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription. + Dan Berrios + modified from Wikipedia + cDNA library - + - - - A family tree is a type of genealogical record. - A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption. - MIABIS - Sarah Bost - genealogical record + + + ordinal value specification + + A categorical value specification in which the available categories were created with an explicit order. + https://en.wikipedia.org/wiki/Ordinal_data provides references for follow-up, but more than one OBI developer has objected to "...whose levels have natural, ordered categories and the distances between those categories is not known..." + +Separate from that, an OBI mechanism for asserting the order of ordinal values specification levels with OWL has not been determined yet. + Mark Andrew Miller, ORCID:0000-0001-9076-6066 + Bjoern Peters in https://github.com/obi-ontology/obi/issues/862 + https://github.com/obi-ontology/obi/issues/862 + ordinal value specification - + - - - The Social Security Administration's Death Master File is a national registry in the United States. - An information content entity that contains information about a nationwide group of individuals. - MIABIS - Sarah Bost - MIABIS contributors - national registry + + + + + + + + + + + + + + + ribosomal RNA-depleted RNA sequencing assay + + An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + rRNA-deleted RNA sequencing assay + PMID:29556074 + CFDE + ribosomal RNA-depleted RNA sequencing assay - + - - - The Care Register for Health Care, maintained by the Finnish National Institute for Health and Welfare, is a national biomedical registry. - A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes. - MIABIS - Sarah Bost - MIABIS contributors - national biomedical registry + + + + + + + + + metatranscriptome sequencing assay + + An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:31450270 + CFDE + metatranscriptome sequencing assay - + - - - Site-directed mutagenesis was used to prepare mutants of the Hypoxia-inducible factor-1 (HIF-1) alpha subunit to investigate the role of certain amino acids in hypoxia. (PMID:12393189) - - An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer. + + + lipid profiling assay + + An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. + Michelle Giglio Rebecca Jackson - url:https://www.ncbi.nlm.nih.gov/books/NBK21945/ - https://github.com/obi-ontology/obi/issues/1058 - site-directed mutagenesis + Suvarna Nadendla + lipidomic assay + OBI metabolite profiling assay + CFDE + lipid profiling assay - + - - - Error-prone PCR was used to introduce amino acid mutations to the cAMP receptor protein (CRP) of E. coli to investigate strain engineering to improve osmotolerance for industrial requirements. (PMID:22179860) - - An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR. - Rebecca Jackson - PMID:15153637 - https://github.com/obi-ontology/obi/issues/1058 - random mutagenesis + + + single-nucleus ATAC-seq + snATAC-seq can be used to dissect heterogeneity and delineate gene regulatory sequences in complex tissues, and uncover both the cell types and the regulatory elements in each cell type without prior knowledge. + + An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. + Mark Andrew Miller, ORCID:0000-0001-9076-6066 + snATAC-seq + http://www.biorxiv.org/content/early/2017/07/06/159137 + https://github.com/obi-ontology/obi/issues/864 + ENCODE + single-nucleus ATAC-seq - + - - + + - + - - - - - - - - - + + - - - - - - - + + - "In an attempt to define the mechanism of insulin-regulated glucose transporter 4 (Glut4) translocation, we have developed an in vitro reconstitution assay... insulin-induced Glut4 translocation can be reconstituted in vitro to a limited extent by using isolated membranes." (PMID:10611313) - - An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. - Rebecca Jackson - reconstitution experiment - url:https://jcs.biologists.org/content/132/4/jcs227488 - https://github.com/obi-ontology/obi/issues/1059 - reconstitution assay + 16s ribosomal gene sequencing assay + + An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + 16S rRNA sequencing assay + PMID:31450270 + CFDE + 16s ribosomal gene sequencing assay - + - - - - - - - - - - - - - - An in vitro reconstituted mouse transcription system helped identify an NF-Y interacting promoter as essential for high-level expression from the R2 promoter. (PMID:11502214) - - A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. - Rebecca Jackson - PMID:9237163 - https://github.com/obi-ontology/obi/issues/1059 - in vitro transcription reconstitution assay + + + single-cell ATAC-seq + + An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. + Mark Andrew Miller, ORCID:0000-0001-9076-6066 + scATAC-seq + http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html + https://github.com/obi-ontology/obi/issues/864 + ENCODE + single-cell ATAC-seq - + - - - - A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. - Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). - Rebecca Jackson - WMS - Bjoern Peters - Michelle Giglio - https://github.com/obi-ontology/obi/issues/1056 - whole metagenome sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + microbiome protein expression profiling assay + + A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + metaproteomic assay + PMID:31450270 + CFDE + microbiome protein expression profiling assay - + - - - A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants. - John Judkins, Bjoern Peters - Wikipedia, OBI - case-control study design + + + cytokine assay + + An analyte assay to study presence, concentration, or amount of cytokines. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:23603216 + CFDE + cytokine assay - + - - - - A genetic transformation which reduces the expression of a specific gene or genes in an organism. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + amplicon sequencing assay + + A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. + Michelle Giglio Rebecca Jackson - gene knock-down - url:https://en.wikipedia.org/wiki/Gene_knockdown - gene knockdown + Suvarna Nadendla + PMID:29628929 + PMID:31450270 + CFDE + amplicon sequencing assay - + - - - - - - - - - - A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease. + + + whole virome sequencing assay + + A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. + Michelle Giglio Rebecca Jackson - RNA interference gene knockdown - url:https://en.wikipedia.org/wiki/Gene_knockdown - RNAi gene knockdown + Suvarna Nadendla + OBI:0002623 + CFDE + whole virome sequencing assay - + - - - ribosomal RNA-depleted RNA extract - Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. - - An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). - Dan Berrios - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 - ribosomal RNA-depleted RNA extract + + + karyotype information + + A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell. + Jie Zheng + EFO_0004426 karyotype + https://github.com/obi-ontology/obi/issues/1097 + VEuPathDB + karyotype information - + - - + + - - + + - "Here, we described the development of RNAi by micro-injection of double-stranded RNA (dsRNA) in the pea aphid Acyrthosiphon pisum. Injection of dsRNA into whole aphid body induced the silencing of two marker genes with different expression patterns: the ubiquitously expressed Ap-crt genes encoding a calreticulin and the gut specific Ap-cath-L gene encoding a cathepsin-L." (PMID:17903251) - - A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. - Rebecca Jackson - RNA interference knockdown assay - RNAi gene knockdown assay - Rebecca Jackson - https://github.com/obi-ontology/obi/issues/1057 - RNAi knockdown assay + partial karyotype information + + A karyotype information that is about the structural variation of partial genome rather than whole genome. + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1097 + VEuPathDB + partial karyotype information - + - - - - An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. - Dan Berrios - DRS - direct RNA-seq - url:https://www.nature.com/articles/nature08390 - https://github.com/obi-ontology/obi/issues/874 - jahilton - direct RNA sequencing assay + + + full karyotype information + + A karyotype information that is about the structural variation of the whole genome. + Jie Zheng + OBI group + https://github.com/obi-ontology/obi/issues/1097 + full karyotype information - + - - - - - - - - - Illumina NovaSeq 6000 - Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. - Dan Berrios - NovaSeq 6000 - http://www.illumina.com/systems/sequencing-platforms/novaseq.html - Illumina NovaSeq 6000 + + + presence or over-threshold value specification + + An ordinal value specification that indicates that either +a) an analyte or mesaurand is present in an evaluant, or +b) that the amount of analyte/measurand detected is over some predetermined threshold. + Mark Andrew Miller, ORCID:0000-0001-9076-6066 + LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 32 + https://github.com/obi-ontology/obi/issues/1202 + bump + presence or over-threshold value specification - + - - - Single-cell RNA sequencing (scRNA-seq) assays provide the expression profiles of individual cells. - - An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin. - Dan Berrios - scRNA-seq - Anna Maria Masci - single-cell RNA sequencing assay + + + single-value binding of antibody with reporter to antigen assay + Detection of SARS-CoV-2 IgG antibodies by an immunoassay method, such as enzyme-linked immunosorbent assay. This test is used in conjunction with SARS-CoV-2 IgA and IgM to aid in the diagnosis of COVID-19 and in the identification of individuals infected with SARS-CoV-2. + + An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest + LOINC indicates that this class would not include flow cytometry or any technique that can determine the localization of an analyte, such as peroxidase immune staining or indirect immunofluorescence (IFA) + Mark Andrew Miller, ORCID:0000-0001-9076-6066 + IA + immunoassay + LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 47 + https://github.com/obi-ontology/obi/issues/1203 + single-value binding of antibody with reporter to antigen assay - + - - - PacBio Sequel - The cDNAs were sequenced on the PacBio Sequel platform. - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation - Bonita Lam - Dan Berrios - Pacific BioSciences Sequel - http://www.pacb.com/products-and-services/pacbio-systems/sequel/ - PacBio Sequel + + + platelet-poor plasma specimen + + A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. + PERSON: Matthew Diller + platelet-poor plasma specimen - + - - - PacBio Sequel II - The cDNAs were sequenced on the PacBio Sequel II platform. - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. - Bonita Lam - Dan Berrios - Pacific BioSciences Sequel II - http://www.pacb.com/products-and-services/pacbio-systems/sequel/ - PacBio Sequel II + + + platelet-poor plasma preparation process + + A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm. + PERSON: Matthew Diller + platelet-poor plasma preparation process - - - - - - - - - - - - - - - - - - - - - - An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - disease exacerbation after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells + + + + + cytometry analysis by automated gating + + A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by an algorithm in order to quantify the frequency of different cell populations of interest. + Bjoern Peters + CMI-PB + https://github.com/obi-ontology/obi/issues/1226 + cytometry analysis by automated gating - + - - - - - - - - - - - - - - - - - - - - An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - decreased disease after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells + + + cytometry analysis by manual gating + + A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by a human operator in order to quantify the frequency of different cell populations of interest. + Bjoern Peters + CMI-PB + https://github.com/obi-ontology/obi/issues/1226 + cytometry analysis by manual gating - + - - + + - + - + - - + + + + + - - An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - decreased disease after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells + + tracheal aspirate specimen + + A specimen that is collected with a suctioning tube from the trachea. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + tracheal wash specimen + PMID:25338241 + tracheal aspirate specimen - + - + - + - + - - + + + + + @@ -65679,29 +82830,33 @@ https://www.doi.org/ - An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - protection from challenge after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells + mid-turbinate nasal swab specimen + + A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 + mid-turbinate nasal swab specimen - + - + - + - + - - + + + + + @@ -65709,55 +82864,34 @@ https://www.doi.org/ - An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - protection from challenge after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells - - - - - - - - - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - pathogen burden after challenge after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden - - - - - - - - - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - pathogen burden after challenge after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden + nasal aspirate specimen + + A specimen that is collected with a suctioning tube from the nasal cavity. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + nasal wash specimen|nasopharyngeal aspirate + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + nasal aspirate specimen - + - + - + - + - - + + + + + @@ -65765,29 +82899,34 @@ https://www.doi.org/ - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - survival from challenge after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival + lower respiratory tract aspirate specimen + + A specimen that is collected with a suctioning tube from the lower respiratory tract. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + lower respiratory tract wash specimen + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + lower respiratory tract aspirate specimen - + - + - + - + - - + + + + + @@ -65795,55 +82934,33 @@ https://www.doi.org/ - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - survival from challenge after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival - - - - - - - - - A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - tumor burden after challenge after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells - - - - - - - - - A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - tumor burden after challenge after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + upper respiratory specimen + + A specimen that is derived from the upper respiratory tract + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + upper respiratory specimen - + - + - + - + - - + + + + + @@ -65851,29 +82968,33 @@ https://www.doi.org/ - An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - tolerance after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells + lower respiratory tract specimen + + A specimen that is derived from the lower respiratory tract. + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + lower respiratory tract specimen - + - + - + - + - - + + + + + @@ -65881,2449 +83002,1642 @@ https://www.doi.org/ - An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - tolerance after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells + anterior nasal swab specimen + + A specimen that is derived from the anterior nasal wall + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + anterior nasal swab specimen - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs + + + aspiration specimen collection - An assay that uses a Giemsa stain to characterize cells. - Chris Stoeckert - Jie Zheng - https://github.com/obi-ontology/obi/issues/1093 - VEuPathDB - Giemsa stain assay + Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. + Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + aspiration procedure + https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C15631 + aspiration specimen collection - + - - - - - - 1 - - - - A specimen composed of an individual organism to be studied in an investigation. - Person: Jie Zheng - EFO_0000542 individual - https://github.com/obi-ontology/obi/issues/1092 - individual organism specimen + + + personal protective device + Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. + PPE is equipment worn by a worker to minimize exposure to specific hazards. + + A device which is a wearable garment designed to protect the wearer's body from injury or infection. + https://orcid.org/0000-0002-8844-9165 + PPE + personal protective equipment + https://en.wikipedia.org/wiki/Personal_protective_equipment + https://github.com/obi-ontology/obi/issues/1193 + personal protective device - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism identification assay that identifies a microorganism in a blood specimen. - John Judkins - https://github.com/obi-ontology/obi/issues/1064 - blood microbiology assay + + + face mask + A systematic review on the efficacy of face coverings against respiratory viruses analyzed 19 randomized trials and concluded that use of face masks and respirators appeared to be protective in both health care and community settings + + A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles. + https://orcid.org/0000-0002-8844-9165 + face covering + respirator + Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask + https://github.com/obi-ontology/obi/issues/1193 + face mask - + - - - - - - - - - - - - - - - - - - - - - Biopsy of a potentially cancerous mole. + + + non-medical mask + A non-medical mask may contain fabrics that are not regulated for use in surgical masks or respirators, or may not be designed to form a seal around the nose and mouth. - A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. - Damion Dooley - Nicole Vasilevsky - https://en.wikipedia.org/wiki/Biopsy - biopsy + A face mask not manufactured according to medical equipment standards. + https://orcid.org/0000-0002-8844-9165 + cloth mask + https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html + https://github.com/obi-ontology/obi/issues/1193 + non-medical mask - + - - - Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland. + + + medical mask + The finding of a much higher rate of infection in the cloth mask arm could be interpreted as harm caused by cloth masks, efficacy of medical masks, or most likely a combination of both. - A biopsy which uses an imaging procedure to guide a needle biopsy. - Damion Dooley - image guided needle biopsy - image-guided biopsy - imaging guided biopsy - https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 - image guided biopsy + A face mask manufactured according to a recognized medical equipment standard. + https://orcid.org/0000-0002-9578-0788 + surgical mask + https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html + https://github.com/obi-ontology/obi/issues/1193 + medical mask - + - - - - - - - - - A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle. + + + N95 respirator - A needle biopsy guided by real-time computed tomography (CT) scan images. - Damion Dooley - CT Assisted Biopsy - CT Guided Biopsy - Computed Tomography Assisted Biopsy - Computed Tomography-Guided Needle Biopsy - http://purl.obolibrary.org/obo/NCIT_C137909 - computed tomography assisted biopsy + A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles. + https://orcid.org/0000-0002-8844-9165 + N95 + N95 face mask + N95 facemask + N95 respirator mask + https://en.wikipedia.org/wiki/N95_mask + https://github.com/obi-ontology/obi/issues/1193 + N95 respirator - + - - - An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid. + + + face shield - A needle biopsy guided by ultrasound visualization. - Damion Dooley - https://www.oncolink.org/cancer-treatment/procedures-diagnostic-tests/biopsy-procedures/ultrasound-guided-needle-biopsy - ultrasound-guided needle biopsy + A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials. + https://orcid.org/0000-0002-8844-9165 + faceshield + splash shield + https://en.wikipedia.org/wiki/Face_shield + https://github.com/obi-ontology/obi/issues/1193 + face shield - + - - - - - - - - - A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin. + + + patient gown - A biopsy that uses a hollow needle to extract cells. - Damion Dooley - https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749 - needle biopsy + A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff. + https://orcid.org/0000-0002-8844-9165 + hospital gown + https://en.wikipedia.org/wiki/Patient_gown + https://github.com/obi-ontology/obi/issues/1193 + patient gown - + - - - A fine needle aspiration biopsy is commonly performed in order to test for cancer. + + + scrubs + Examples consist of a short-sleeve V-necked shirt and drawstring pants or a short-sleeve calf-length dress, a tie-back or bouffant-style cap, a mask, a surgical gown, latex gloves, and supportive closed-toe shoes. - A biopsy that uses a thin needle to extract cells. - Chris Stoeckert, Helena Ellis, Jie Zheng - FNA - FNAB - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ - NCI BBRB - fine needle aspiration biopsy + A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap. + https://orcid.org/0000-0002-8844-9165 + scrub clothing item + https://en.wikipedia.org/wiki/Scrubs_(clothing) + https://github.com/obi-ontology/obi/issues/1193 + scrubs - + - - - A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed. + + + reusable patient gown - A biopsy that uses a hollow tube to collect a core of tissue. - Chris Stoeckert, Helena Ellis, Jie Zheng - CNB - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ - NCI BBRB - core needle biopsy + A patient gown intended to be reused after being laundered. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Patient_gown + https://github.com/obi-ontology/obi/issues/1193 + reusable patient gown - + - - - Surgical biopsy may be required to collect hard-to-reach tissue. + + + disposable patient gown - A biopsy involving a surgical incision into an organism to access the biopsy material. - Damion Dooley - excisional biopsy - open biopsy - https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 - surgical biopsy + A patient gown intended for a single period of continuous use and then disposed of. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Patient_gown + https://github.com/obi-ontology/obi/issues/1193 + disposable patient gown - + - - - - - - - - - The makeup of fat in the abdominal wall can be investigated by fat biopsy. + + + medical gown - A biopsy involving the collection of a small part of the abdominal wall fat pad. - Nicole Vasilevsky, Damion Dooley - abdominal wall biopsy - fat biopsy - https://www.ucsfbenioffchildrens.org/tests/003841.html - abdominal wall fat pad biopsy + A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional. + https://orcid.org/0000-0002-8844-9165 + hospital gown + https://en.wikipedia.org/wiki/Medical_gown + https://github.com/obi-ontology/obi/issues/1193 + medical gown - + - - - - - - - - - A mouse tail biopsy was performed to collect material for DNA extraction. + + + apron - A biopsy involving the collection of the tip of a mamallian tail. - Nicole Vasilevsky, Damion Dooley - snip - http://web.jhu.edu/animalcare/policies/Tail%20Biopsy%20of%20Mice.pdf - tail biopsy + A garment which is worn over other clothing and covers mainly the front of the body. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Apron + https://github.com/obi-ontology/obi/issues/1193 + apron - + - - - - - - - - - A bone marrow biopsy removes bone with the marrow inside to look at under a microscope + + + surgical gown - A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected. - Nicole Vasilevsky - http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy - bone marrow biopsy + A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + surgical gown - + - - - - - - - - - A three or four millimeter punch is used in s skinpunch biopsy proceedure. + + + personal protective glove - A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool. - Nicole Vasilevsky - punch biopsy; skin biopsy - http://healthlibrary.epnet.com/GetContent.aspx?token=b93d114e-5009-4f6a-9917-6c594254fcc7&chunkiid=14861 - skinpunch biopsy + A personal protective device which is a glove. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + personal protective glove - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-15 production by T cells. - IEDB - IEDB - IL-15 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-15 production by T cells + + + personal protective clothing item + + A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + personal protective clothing item + + + + + + + + + laboratory coat + + A personal protective clothing item which is an overcoat worn by medical or laboratory professionals. + https://orcid.org/0000-0002-8844-9165 + white coat + https://en.wikipedia.org/wiki/White_coat + https://github.com/obi-ontology/obi/issues/1193 + laboratory coat - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cytometric bead array assay that detects interleukin-16 production by T cells. - IEDB - IEDB - IL-16 release|cytometric bead array - cytometric bead array assay measuring epitope specific interleukin-16 production by T cells + + + medical glove + + A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Medical_glove + https://github.com/obi-ontology/obi/issues/1193 + medical glove - + - - - - - - - - - - - - - - An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - hypersensitivity after adoptive transfer|in vivo assay - in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells + + + nitrile glove + + A personal protective glove which is made out of nitrile rubber. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Medical_glove + https://github.com/obi-ontology/obi/issues/1193 + nitrile glove - + - - - - - - - - - - - - - - An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - type IV hypersensitivity (DTH) after adoptive transfer|in vivo skin test - in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells + + + transparent partition + + A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. + https://orcid.org/0000-0002-8844-9165 + transparent partition + https://ncceh.ca/content/blog/physical-barriers-covid-19-infection-prevention-and-control-commercial-settings + https://github.com/obi-ontology/obi/issues/1193 + transparent droplet barrier - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - proliferation after adoptive transfer|in vivo assay - in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells + + + footwear cover + + A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants. + https://orcid.org/0000-0002-8844-9165 + boot cover + shoe cover + https://en.wiktionary.org/wiki/shoecover + https://github.com/obi-ontology/obi/issues/1193 + footwear cover - + - - - - - - - - - - - - - - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - antibody help after adoptive transfer|biological activity - biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells + + + disposable footwear cover + + A footwear cover which is designed for a single period of continuous use and then disposed of. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + disposable footwear cover - + - - - - - - - - - - - - - - A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - T cell help after adoptive transfer|biological activity - biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells + + + reusable footwear cover + + A footwear cover which is designed for repeated use. + https://orcid.org/0000-0002-8844-9165 + OBI + https://github.com/obi-ontology/obi/issues/1193 + reusable footwear cover - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - cytotoxicity after adoptive transfer|in vivo assay - in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells + + + surgical N95 respirator + + A N95 respirator which has been approved by the FDA as a surgical mask. + https://orcid.org/0000-0002-8844-9165 + healthcare respirator + medical respirator + surgical N95 + surgical N95 respirator + https://multimedia.3m.com/mws/media/1794572O/surgical-n95-vs-standard-n95-which-to-consider.pdf + https://github.com/obi-ontology/obi/issues/1193 + surgical N95 respirator - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells. - IEDB - IEDB - perforin release|ELISA - ELISA measuring epitope specific perforin release by T cells + + + protective coverall + + A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination. + https://orcid.org/0000-0002-8844-9165 + https://www.safeopedia.com/definition/863/disposable-coveralls + https://github.com/obi-ontology/obi/issues/1193 + protective coverall - + - - - Selenite broth is an enrichment culture medium used to selectively isolate Salmonella species. + + + protective sleeve + A protective sleeve can be designed to provide protection from heat, welding spatter or hot metal, chemicals, sharp objects, paint or other liquids. - A culture medium that is designed to favor the growth of a particular microorganism or cells over others, enriching a sample for the microorganism or cells of interest. - - - isolation medium - - 2020-03-08T22:04:07Z - enrichment culture medium - + A personal protective clothing item which is a protective cover worn over the arm. + https://orcid.org/0000-0002-8844-9165 + https://www.safeopedia.com/definition/974/protective-sleeves + https://github.com/obi-ontology/obi/issues/1193 + protective sleeve - + - - - case series study design - PMID: 22213493 + + + protective apron - A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included. - http://orcid.org/0000-0002-8844-9165 - https://www.ncbi.nlm.nih.gov/pubmed/22213493 - case series design + A personal protective clothing item which is an apron. + https://orcid.org/0000-0002-8844-9165 + https://en.wikipedia.org/wiki/Apron + https://github.com/obi-ontology/obi/issues/1193 + protective apron - + - - + + + medical cap - An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. - Damion Dooley - MPRA - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364389/ - massively parallel reporter assay + A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp. + https://orcid.org/0000-0002-8844-9165 + bouffant cap + bouffant hat + medical bonnet + scrub cap + surgical hat + https://en.wikipedia.org/wiki/Scrubs_(clothing) + https://github.com/obi-ontology/obi/issues/1193 + medical cap - + - - - - - - - - - An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - in vivo response after adoptive transfer|in vivo assay - in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells + + + specimen collection device + + A container used to collect a specimen. + https://orcid.org/0000-0002-8844-9165 + specimen collection device - + - - - - - - - - - An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells. - IEDB - IEDB - in vivo response after adoptive transfer|in vivo assay - in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells + + + chromatography vial + + A vial with cap and container material suited to optical, sanitary and handling requirements of chromatography. + PERSON:Daniel Schober + GROUP:<http://msi-ontology.sourceforge.net> + http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 + chromatography vial - + - - - - - - - - - - - - - - - - - - - - An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specfic T cells. - IEDB - IEDB - disease exacerbation after adoptive transfer|in vivo assay - in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells + + + specimen pad + An absorbent pad and its accompanying container are designed to provide safe storage and transport to various degrees for diagnostic and clinical samples, infectious and hazardous materials, chemicals, pharmaceuticals and environmental samples. + + A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter. + https://orcid.org/0000-0002-8844-9165 + absorbant pad + polysponge + sample pad + sampling sponge + specimen sponge + surface wipe + swab + Derived from NCIT sponge definition. + specimen pad - + - - - - - - - - - vacuum-assisted biopsy needle - Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source. - - A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material. - Damion Dooley - https://www.researchgate.net/publication/330227873 - https://github.com/obi-ontology/obi/issues/1163 - vacuum-assisted biopsy needle + + + specimen collection swab stick + A swab stick allows a worker to collect samples without touching the inside of the bag + + A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material. + https://orcid.org/0000-0002-8844-9165 + polyprobe + sponge probe + sponge stick + sponge-stick + https://medical-dictionary.thefreedictionary.com/swab + specimen collection swab stick - + - - - “Inhibition of MERS-CoV-spike-mediated pseudovirus entry by the HKU4 S1 domain “ (from https://doi.org/10.1073/pnas.1405889111); “protease treatment did not enhance pseudotype entry in the absence of host receptor “; “bat-derived cell lines derived from other species were infected with VSV-reporter particles pseudotyped with chimeric spikes and luciferase was measured as readout for cell entry” (from https://doi.org/10.1038/s41564-020-0688-y) ; “teicoplanin could inhibit the entry of HIV-1-2019-nCoV-S pseudoviruses with the IC50 value of 1.66 uM” (from https://doi.org/10.1101/2020.02.05.935387) + + + cotton swab - An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. - Thomas Lemberger - pseudotype cell entry - pseudotype entry - pseudotyped particle cell entry assay - pseudovirus cell entry - Figure 1c in https://doi.org/10.1038/s41564-020-0688-y or Materials & Method in https://www.pnas.org/content/111/34/12516 - pseudovirus entry assay + A device which is a cotton pad mounted on one or both ends of a stick. + https://orcid.org/0000-0002-8844-9165 + Q-tip + swab-sampler + https://en.wikipedia.org/wiki/Cotton_swab + cotton swab - + - - + + - - + + - glass bottle - - A container with a narrow neck that is made of glass. - VEuPathDB - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - glass bottle + drag swab + + A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string + https://orcid.org/0000-0002-8844-9165 + https://www.fda.gov/food/laboratory-methods-food/environmental-sampling-and-detection-salmonella-poultry-houses + drag swab - + - - - - - - - - - glass bottle coated with insecticides - - A glass bottle that coated with material designed to control insects. - VEuPathDB - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - glass bottle coated with insecticides + + + pre-moistened swab stick + + A specimen collection swab stick that is pre-moistened with liquid prior to sampling. + https://orcid.org/0000-0002-8844-9165 + pre-moistened swab stick - + - - - - A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). - Jie Zheng - short interspersed elements PCR - PMID: 12711348 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - short interspersed nuclear elements polymerase chain reaction + + + surface wipe + Surface sampling procedures involved the use of polyester wipes, swabs, contact slides (two types), and adhesive tapes; a gelatin filter was used to sample the air. + + A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces. + https://orcid.org/0000-0002-8844-9165 + https://www.science.gov/topicpages/s/surface+wipe+sampling.html + surface wipe - + - - - - A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction. - Jie Zheng - nested-PCR - nested PCR - https://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - nested polymerase chain reaction + + + catheter + A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. + + A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body. + https://orcid.org/0000-0002-8844-9165 + http://purl.bioontology.org/ontology/MESH/D057785 + catheter - + - - + + + surveillance process - An electrophoresis that separates and characterize proteins based on reaction with antibodies. - Jie Zheng - IEP - https://en.wikipedia.org/wiki/Immunoelectrophoresis - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - immunoelectrophoresis + An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. + Chris Stoeckert + Shane Babcock, OBI + https://github.com/obi-ontology/obi/issues/1181 + IDO, VEuPathDB + surveillance process - + - - + + + cluster study group role + A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound. - An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions. - Jie Zheng - http://www.ispybio.com/search/protocols/ie%20protocol2.pdf - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - counter current immunoelectrophoresis + A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. + Chris Stoeckert, Brianna Lindsay + cluster study arm + ClinEpiDB + cluster study group role - + - - + + + compound study group role + A compound study group consisting of geographically proximate households that share a common water source. - A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product. - Jie Zheng - LDR - MIRO:20000103 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - ligase detection reaction + A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. + Chris Stoeckert, Brianna Lindsay + compound study arm + ClinEpiDB + compound study group role - + - - - - An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR. - Jie Zheng - LAMP - https://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - loop-mediated isothermal amplification + + + ultraviolet light source + + A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. + Person: Jie Zheng + UV light source + Person: Jie Zheng + https://github.com/obi-ontology/obi/issues/1200 + VEuPathDB + ultraviolet light source - + - - - - An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - detection of pathogenic organisms objective + + + visible light source + + A light source that provides visible light for use in a distant area using a delivery system. + Person: Jie Zheng + Person: Jie Zheng + https://github.com/obi-ontology/obi/issues/1200 + VEuPathDB + visible light source - + - - - - An organism feature identification objective that aims to detect insecticide resistance of an insect. - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance detection objective + + + solar light source + + A light source that light is produced from solar energy. + Person: Chris Stoeckert + Person: Jie Zheng + Person: Chris Stoeckert + Person: Jie Zheng + https://github.com/obi-ontology/obi/issues/1200 + VEuPathDB + solar light source - + - - - A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. + + + adult arthropod specimen collection process - A specimen of the blood ingested by an arthropod. - The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. - Chris Stoeckert - Jie Zheng - blood meal - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - arthropod meal of blood specimen + A live arthropod specimen collection process in which the arthropods are in the adult stage. + John Judkins + collection of adults + MIRO:30000052 + https://github.com/obi-ontology/obi/issues/1217 + adult arthropod specimen collection process - + - - - - - - - - - - - - + + + animal-biting arthropod specimen collection by aspiration - An assay that uses polymerase chain reaction technique to amplify DNA. - VEuPathDB - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - polymerase chain reaction assay + An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. + John Judkins + animal biting catch + MIRO:30000012 + https://github.com/obi-ontology/obi/issues/1217 + animal-biting arthropod specimen collection by aspiration - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + animal-biting outdoor arthropod specimen collection by aspiration - An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. - VEuPathDB - RFLP - restriction fragment length polymorphism - restriction fragment length polymorphism analysis - https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - restriction fragment length polymorphism assay + An animal-biting arthropod specimen collection by aspiration that occurs outside a building. + John Judkins + animal biting catch - outdoors + MIRO:30000014 + https://github.com/obi-ontology/obi/issues/1217 + animal-biting outdoor arthropod specimen collection by aspiration - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + aquatic arthropod specimen collection process - An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. - VEuPathDB - DNA finger printing - DNA fingerprint - DNA fingerprinting - DNA profiling - VEuPathDB - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - DNA fingerprinting assay + An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. + John Judkins + aquatic environment catch + MIRO:30000048 + https://github.com/obi-ontology/obi/issues/1217 + aquatic arthropod specimen collection process - + - - - - - - - - - - - - + + + arthropod resting in animal house specimen collection by aspiration - An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. - VEuPathDB - resistance identification/monitoring - MIRO:20000001 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance assay + An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. + John Judkins + animal shed resting catch + MIRO:30000027 + https://github.com/obi-ontology/obi/issues/1217 + arthropod resting in animal house specimen collection by aspiration - + - - - - - - - - + + + arthropod resting outdoors on artificial support specimen collection by aspiration - An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. - VEuPathDB - monitoring known mutations - MIRO:20000096 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by monitoring known mutations assay + An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture. + John Judkins + outdoors shelter catch - artificial + MIRO:30000026 + https://github.com/obi-ontology/obi/issues/1217 + arthropod resting outdoors on artificial support specimen collection by aspiration - + - - - - - - - - - - - - - - - - - - - + + + arthropod resting outdoors on natural support specimen collection by aspiration - An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. - VEuPathDB - metabolic resistance assay - MIRO:20000003 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by detecting enzyme activity assay + An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant. + John Judkins + outdoors shelter catch - natural + MIRO:30000025 + https://github.com/obi-ontology/obi/issues/1217 + arthropod resting outdoors on natural support specimen collection by aspiration - + - - - - - - - - + + + arthropod resting outdoors specimen collection by aspiration - An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. - VEuPathDB - bioassay - MIRO:20000058 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance bioassay + An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity. + John Judkins + outdoors shelter catch + MIRO:30000024 + https://github.com/obi-ontology/obi/issues/1217 + arthropod resting outdoors specimen collection by aspiration - + - - - - - - - - - - - - - - - - - - - + + + arthropod specimen collection by aspiration - An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. - VEuPathDB - alpha esterase activity assay - IRO:0000149 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by detecting alpha esterase activity assay + A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container. + John Judkins + catch by aspiration + MIRO:30000043 + https://github.com/obi-ontology/obi/issues/1217 + arthropod specimen collection by aspiration - + - - - - - - - - - - - - - - - - - - - + + + arthropod specimen collection process - An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. - VEuPathDB - beta esterase activity assay - IRO:0000150 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by detecting beta esterase activity assay + A specimen collection process that has the objective of collecting arthropods as specimens. + John Judkins + collection of arthropods + field population catch + MIRO:30000044 + https://github.com/obi-ontology/obi/issues/1217 + arthropod specimen collection process - + - - - - - - - - - - - - - - - - - - - + + + human-biting arthropod specimen collection by aspiration - An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. - VEuPathDB - AChE activity assay - AChE assay - acetylcholinesterase assay - MIRO:20000010 - MIRO:20000084 - MIRO:20000086 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by detecting acetylcholinesterase activity assay + An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. + John Judkins + man biting catch + MIRO:30000017 + https://github.com/obi-ontology/obi/issues/1217 + human-biting arthropod specimen collection by aspiration - + - - - - - - - - - - - - - - - - - - - + + + human-biting indoor arthropod specimen collection by aspiration - An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). - VEuPathDB - GST related assay - MIRO:20000083 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by detecting glutathione S-transferase activity assay + An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. + John Judkins + man biting catch - indoors + MIRO:30000019 + https://github.com/obi-ontology/obi/issues/1217 + human-biting indoor arthropod specimen collection by aspiration - + - - - - - - - - - - - - - - - - - - - + + + human-biting outdoor arthropod specimen collection by aspiration - An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. - VEuPathDB - pNPA assay - MIRO:20000019 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by detecting carboxylic ester hydrolase activity assay + An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building. + John Judkins + man biting catch - outdoors + MIRO:30000018 + https://github.com/obi-ontology/obi/issues/1217 + human-biting outdoor arthropod specimen collection by aspiration - + - - - - - - - - + + + knockdown arthropod specimen collection by pyrethrum spray - An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. - VEuPathDB - mixed-function oxidase assay - MIRO:20000062 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by detecting mixed-function oxidase assay + A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. + John Judkins + pyrethrum spray catch + MIRO:30000023 + https://github.com/obi-ontology/obi/issues/1217 + knockdown arthropod specimen collection by pyrethrum spray - + - - - - - - - - + + + knockdown arthropod specimen collection process - An insecticide resistance bioassay without the use of any synergist. - VEuPathDB - direct bioassay - MIRO:20000044 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - direct insecticide resistance bioassay + An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. + John Judkins + knockdown collection + IRO:0000014 + https://github.com/obi-ontology/obi/issues/1217 + knockdown arthropod specimen collection process - + - - - - - - - - + + + live arthropod specimen collection process - An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. - VEuPathDB - topical application assay - IRO:0000155 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - topical application insecticide resistance bioassay + An arthropod specimen collection process meant to collect live specimens. + John Judkins + catch of live specimens + MIRO:30000044 + VSMO:0001445 + https://github.com/obi-ontology/obi/issues/1217 + live arthropod specimen collection process - + - - - - - - - - + + + arthropod trap - A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. - VEuPathDB - diagnostic test - MIRO:20000075 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - direct insecticide resistance diagnostic assay + A device designed to catch arthropods. + John Judkins + MIRO:30000011 + https://github.com/obi-ontology/obi/issues/1217 + arthropod trap - + - - - - - - - - + + + artificial pit shelter - A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. - VEuPathDB - dose response test - MIRO:20000076 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance dose response assay + An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected. + John Judkins + IRO:0000005 + https://github.com/obi-ontology/obi/issues/1217 + artificial pit shelter - + - - - - - - - - + + + baited net trap + + An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal. + John Judkins + https://github.com/obi-ontology/obi/issues/1217 + baited net trap + + + + + + + + + barrier trap - A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. - VEuPathDB - time response test - MIRO:20000013 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance time response assay + An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. + John Judkins + IRO:0000017 + https://github.com/obi-ontology/obi/issues/1217 + barrier trap - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + + BG-Counter - A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. - VEuPathDB - CDC bottle bioassay - MIRO:20000009 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - Centre for Disease Control and Prevention bottle bioassay + A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. + John Judkins + IRO:0000143 + https://github.com/obi-ontology/obi/issues/1217 + BG-Counter - + - - + + - - + + + BG-Sentinel trap - A direct insecticide resistance diagnostic assay uses WHO cone kit. - VEuPathDB - cone DT - MIRO:20000039 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - WHO cone kit diagnostic assay + An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current. + John Judkins + IRO:0000028 + VSMO:0001906 + https://github.com/obi-ontology/obi/issues/1217 + BG-Sentinel trap - + - - - - - - - - + + + Centers for Disease Control and Prevention light trap - A direct insecticide resistance diagnostic assay uses WHO paper kit. - VEuPathDB - WHO paper kit DT - MIRO:20000041 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - WHO paper kit diagnostic assay + A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery. + This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. + John Judkins + CDC light trap + IRO:0000163 + https://github.com/obi-ontology/obi/issues/1217 + Centers for Disease Control and Prevention light trap - + - - - - - - - - + + + dipper for arthropod immatures - A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. - VEuPathDB - WHO larvicide DT - MIRO:20000049 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - WHO larvicide diagnostic assay + A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. + John Judkins + dipper for immatures + VSMO:0001479 + https://github.com/obi-ontology/obi/issues/1217 + dipper for arthropod immatures - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + encephalitis virus surveillance trap + + A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods. + John Judkins + EVS trap + IRO:0000029 + VSMO:0001295 + https://github.com/obi-ontology/obi/issues/1217 + encephalitis virus surveillance trap + + + + + + + + + gravid trap + + An arthropod trap that is designed to collect gravid female arthropods or their eggs. + John Judkins + IRO:0000030 + https://github.com/obi-ontology/obi/issues/1217 + gravid trap + + + + + + + + + light trap + + An arthropod trap that uses light as an attractant. + John Judkins + MIRO:30000065 + https://github.com/obi-ontology/obi/issues/1217 + light trap + + + + + + + + + light trap for indoor use + + A light trap designed to be placed inside a building. + John Judkins + indoor light trap + MIRO:30000009 + https://github.com/obi-ontology/obi/issues/1217 + light trap for indoor use + + + + + + + + + light trap for outdoor use + + A light trap designed to be placed outside a building. + John Judkins + outdoor light trap + MIRO:30000010 + https://github.com/obi-ontology/obi/issues/1217 + light trap for outdoor use + + + + + + + + + Mosquito Magnet Pro trap + + An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. + John Judkins + IRO:0000022 + https://github.com/obi-ontology/obi/issues/1217 + Mosquito Magnet Pro trap + + + + + + + + + MosquiTRAP + + A gravid trap consisting of an arthropod attractant and adhesive surface. + John Judkins + IRO:0000140 + https://github.com/obi-ontology/obi/issues/1217 + MosquiTRAP + + + + + + + + + New Jersey light trap + + A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. + John Judkins + New Jersey trap + IRO:0000031 + https://github.com/obi-ontology/obi/issues/1217 + New Jersey light trap + + + + + + + + + Onderstepoort Veterinary Institute light-suction trap + + A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter. + John Judkins + OVI light-suction trap + IRO:0000154 + Parasites Vectors 8, 239 (2015) + https://github.com/obi-ontology/obi/issues/1217 + Onderstepoort Veterinary Institute light-suction trap + + + + + + + + + outlet window trap - An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. - VEuPathDB - bottle bioassay DR test - MIRO:20000011 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance dose response by bottle assay + An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. + John Judkins + outlet window trap + MIRO:30000020 + https://github.com/obi-ontology/obi/issues/1217 + outlet window trap - + - - - - - - - - + + + ovitrap - An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. - VEuPathDB - WHO larvicide DR test - MIRO:20000050 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance dose response by survival of larvae assay + An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females. + John Judkins + oviposition trap + MIRO:30000016 + VSMO:0001501 + https://github.com/obi-ontology/obi/issues/1217 + ovitrap - + - - - - - - - - + + + resting arthropod trap + + An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. + John Judkins + https://github.com/obi-ontology/obi/issues/1217 + resting arthropod trap + + + + + + + + + resting box trap - An insecticide resistance dose response assay using WHO paper kit. - VEuPathDB - WHO paper kit DR test - MIRO:20000048 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance dose response by WHO paper kit assay + An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. + John Judkins + resting box catch + IRO:0000021 + https://github.com/obi-ontology/obi/issues/1217 + resting box trap - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + resting bucket - An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. - VEuPathDB - bottle bioassay TR test - MIRO:20000030 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance time response by bottle assay + An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host). + John Judkins + resting bucket catch + IRO:0000141 + https://github.com/obi-ontology/obi/issues/1217 + resting bucket - + - - - - - - - - + + + Shannon trap - An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. - VEuPathDB - WHO paper kit TR test - MIRO:20000036 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance time response by WHO paper kit assay + An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap. + John Judkins + shannon trap catch + IRO:0000191 + https://github.com/obi-ontology/obi/issues/1217 + Shannon trap - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + sticky resting bucket - An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations. - VEuPathDB - ARMS - Amplification Refractory Mutation System - IRO:0000006 - PMID: 18428319 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by amplification refractory mutation system assay + An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected. + John Judkins + sticky resting bucket catch + IRO:0000142 + https://github.com/obi-ontology/obi/issues/1217 + sticky resting bucket - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + sticky trap - An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. - VEuPathDB - PIRA-PCR - Primer Introduced Restriction Analysis PCR - polymerase chain reaction-primer-introduced restriction analysis - IRO:0000007 - PMID: 8339229 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by primer introduced restriction analysis PCR assay + An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. + John Judkins + sticky trap catch + IRO:0000128 + https://github.com/obi-ontology/obi/issues/1217 + sticky trap - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + population based design + + A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment. + Chris Stoeckert + https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design + https://github.com/obi-ontology/obi/issues/1090 + population based design + + + + + + + + - + + + + + + + + - - + + + + + + + + + + + + + fluorescence imaging-based apoptosis assay - An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. - VEuPathDB - gene mutation detection by nested PCR - IRO:0000127 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by nested polymerase chain reaction assay + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/1 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based apoptosis assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + + + + + + + + - - + + + + + + + + + + + + + fluorescence imaging-based cell proliferation assay - An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. - VEuPathDB - MIRO:20000103 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by ligase detection reaction assay + A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + fluroescence imaging-based cell count assay + url:http://lincsportal.ccs.miami.edu/beta/assays/31 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell proliferation assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + + + + + + + + - - + + + + + + + + + + + + + fluroescence imaging-based cell cycle state assay - An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. - VEuPathDB - gene mutation detection by LDR-FMA - ligase detection reaction-fluorescent microsphere assay - IRO:0000151 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by ligase detection reaction-fluorescent microsphere assay + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/10 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluroescence imaging-based cell cycle state assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + + + + + + + + - - + + + + + + + + + + + + + fluorescence imaging-based cell viability assay - An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. - VEuPathDB - PASA - PCR amplification of specific alleles - allele-specific amplification and amplification refractory mutation system - PMID: 1734929 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by PCR amplification of specific alleles assay + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/27 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell viability assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + - + + + + + + + + - - + + + + + + + + + + + + + fluorescence imaging-based drug synergy assay - An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. - VEuPathDB - MIRO:20000102 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by fluorogenic PCR assay + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/7 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based drug synergy assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + @@ -68332,598 +84646,576 @@ https://www.doi.org/ - - + + + + + + + + + + + + + fluorescence imaging-based cell morphology assay - An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. - VEuPathDB - PCR-RFLP - MIRO:20000113 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by PCR-RFLP assay + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell morphology assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + + + + + + + + - - + + + + + + + + + + + + + fluorescence imaging multiplex cytological profiling - An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). - VEuPathDB - Short Interspersed Elements PCR - IRO:0000013 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - insecticide resistance by short interspersed elements PCR assay + A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/8 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging multiplex cytological profiling - + - - - - - - - - - - - - - - - - - - - - - + + + protein state assay - An organism identification assay that aims to detect pathogens. - VEuPathDB - pathogen detection method - IRO:0000137 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - pathogen detection assay + A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + protein state assay - + - - + + - + - - - - + + + + + + - - + + + + + + + + + + + + + fluorescence imaging-based protein phosphorylation state assay - A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. - VEuPathDB - VectorTest - IRO:0000138 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - VectorTest assay + A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/15 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based protein phosphorylation state assay - + - - + + - + - - - - + + + + + + - - - - - - + mass spectrometry-based protein state assay - A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. - VEuPathDB - Rapid Analyte Measurement Platform - IRO:0000164 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - pathogen detection by Rapid Analyte Measurement Platform assay + A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + mass spectrometry-based protein state assay - + - - + + + targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay + + A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + P100 phosphoprotein quantification assay + PMID:26912667 + PMID:29655704 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay + + + + + + + + + reverse phase protein array profiling assay + + A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + RPLA assay + RPPA assay + reverse phase lysate array profiling assay + PMID: 17041095 + PMID:31820393 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + reverse phase protein array profiling assay + + + + + + + + - - - - - - - - - - + + + + + + - - - - - - + SWATH-MS protein profiling assay - A pathogen detection assay that is based on loop-mediated isothermal amplification. - VEuPathDB - Loop-mediated isothermal amplification - IRO:0000165 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - pathogen detection by loop-mediated isothermal amplification assay + A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + sequential window acquisition of all theoretical mass spectra protein profiling assay + PMID:30104418 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + SWATH-MS protein profiling assay - + - - - - - - - - - - - - + + + tandem mass tag mass spectrometry assay - An assay that analyzes the specimen taken from blood meal fed organism, such as insect. - VEuPathDB - blood meal analysis - IRO:0000135 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - blood meal assay + A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:12713048 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + tandem mass tag mass spectrometry assay - + - - + + - + + + + + + + + - + + + + + + + + + + + + fluorescence imaging-based reporter gene assay - A blood meal assay that uses a counter current immunoelectrophoresis technique. - VEuPathDB - CIE - countercurrent immunoelectrophoresis - IRO:0000136 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - blood meal by counter current immunoelectrophoresis assay + A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based reporter gene assay - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + - - + + + global chromatin profiling by mass spectrometry assay - A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. - VEuPathDB - DNA based blood meal finger printing - VEuPathDB - VSMO:0001307 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - DNA based blood meal finger printing assay + A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + GCP + global chromatin epigenetic profiling + global chromatin profiling + PMID:25448295 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + global chromatin profiling by mass spectrometry assay - + - - - - - - - - + + + kinase inhibitor assay - An organism identification assay that is based on the size of organism. - VEuPathDB - by size - IRO:0000145 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - organism identification by size assay + A type of assay that identifies compounds that inhibit the activity of kinases. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + kinase inhibitor assay - + - - - - - - - - + + + KINOMEscan assay - An organism identification assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. - VEuPathDB - cross mating experiment - MIRO:30000036 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - organism identification by cross mating assay + A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.discoverx.com/technologies-platforms/competitive-binding-technology/kinomescan-technology-platform + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + KINOMEscan assay - + - - - - - - - - + + + KiNativ assay - An organism identification assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. - VEuPathDB - cytological chromosome examination - MIRO:30000037 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - organism identification by cytological chromosome examination assay + A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.kinativ.com/technology.html + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + KiNativ assay - + - - - - - - - - - - - - - - + + + landmark transcript profiling assay - An organism identification assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. - VEuPathDB - isoenzyme electrophoresis - MIRO:30000038 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - organism identification by isoenzyme electrophoresis assay + A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + L1000 mRNA profiling assay + PMID:29195078 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + landmark transcript profiling assay - + - - - - - - - - + + + microenvironment microarray assay - An organism identification assay that is based on examination of morphology and the use of specific "taxonomic keys" to determine the species of the specimen. - VEuPathDB - morphological examination - MIRO:30000039 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - organism identification by morphological examination assay + A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + MEMA assay + PMID:29199020 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + microenvironment microarray assay - + - - - - - - - - - - - - - - + + + microwestern meso-scale quantitative western blot assay - An organism identification assay that is based on PCR. - VEuPathDB - PCR-based species identification - MIRO:30000040 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - organism identification by PCR assay + A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:28092050 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + microwestern meso-scale quantitative western blot assay - + - - + + - - - - - - - + + + + + + + + + positive/negative ion switching metabolite profiling assay - An organism identification assay that is based on DNA hybrdization. - VEuPathDB - species specific DNA hybridization - MIRO:30000041 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - organism identification by specific DNA hybridization assay + A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + positive/negative ion switching metabolomic assay + PMID:22498707 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + positive/negative ion switching metabolite profiling assay - - - - - - - - - - - + + + + + + cyclic immunoflouroescence assay - An organism identification assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. - VEuPathDB - salinity tolerance tests - MIRO:30000042 - https://github.com/obi-ontology/obi/issues/1117 - VEuPathDB - organism identification by salinity tolerance assay + A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:27925668 + PMID:29993362 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + cyclic immunoflouroescence assay - + - - - molecular label role - A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. - MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role). -JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced REO_0000171 by newly assigned ID: OBI:0002743. - Group: OBI - molecular tracer role - OBI developer call, 3-12-12 - https://github.com/obi-ontology/obi/issues/1135 - molecular label role + + + multiplex bead-based protein state immunoassay + + A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.bio-rad.com/en-us/applications-technologies/multiplex-immunoassays?ID=LUSM0E8UU + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + multiplex bead-based protein state immunoassay - + - - + + - + - - + + + + + + - - - molecular label - A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay - JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744. - Group: OBI - molecular tracer - OBI developer call, 3-12-12 - https://github.com/obi-ontology/obi/issues/1135 - molecular label - - - - - - - - - - - - - - A vacuum assisted biopsy can remove an area of abnormal cells from breast tissue. - - A biopsy performed with a needle augmented with a vacuum device. - Damion Dooley - VAB - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ - vacuum-assisted biopsy + endotracheal tube specimen + + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. + John Judkins ORCID:0000-0001-6595-0902 + https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 + endotracheal tube specimen - + - + @@ -68934,300 +85226,192 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + - A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. - John Judkins - PMC3297553 - induced sputum specimen - - - - - - - - - A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. - John Judkins - https://en.wikipedia.org/wiki/Serial_passage - https://www.merriam-webster.com/dictionary/passage - passage process - - - - - - - - - - - - - - - A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process. - John Judkins - https://en.wikipedia.org/wiki/Serial_passage - https://www.merriam-webster.com/dictionary/passage - passage history record - - - - - - - - - - - - - - - Oxford Nanopore MinION - Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION + endotracheal aspirate specimen - A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. - PERSON: Bonita Lam - ONT MinION, MinION - https://nanoporetech.com/products/minion - Oxford Nanopore MinION + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. + John Judkins ORCID:0000-0001-6595-0902 + https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 + endotracheal aspirate specimen - + - - - - - - - - - Oxford Nanopore GridION Mk1 - Nineteen libraries were constructed and sequenced on nineteen different R9.4 FlowCells using the GridION X5 sequencer + + + input protein sequence start site + When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being analyzed is the input protein sequence start site. - A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually. - PERSON: Bonita Lam - Oxford Nanopore GridION X5, GridION Mk1 - https://nanoporetech.com/products/gridion - Oxford Nanopore GridION Mk1 + The position of the first amino acid in a protein sequence being analyzed (input protein sequence). + Emma Griffiths + input protein start + query protein start site + Emma Griffiths + input protein sequence start site - + - - - - - - - - - Oxford Nanopore PromethION - Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. + + + input protein sequence stop site + When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence being analyzed is the input protein sequence stop site. - A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - PERSON: Bonita Lam - PromethION - https://nanoporetech.com/products/promethion - Oxford Nanopore PromethION - - - - - - - - - - - - - - - Precision nuclear run-on and sequencing to detect Pol II initiation sites - Bonita Lam - PRO-CAP - https://github.com/obi-ontology/obi/issues/1102 - PRO-cap + The position of the last amino acid in a protein sequence being analyzed (input protein sequence). + Emma Griffiths + input protein stop + query protein stop site + Emma Griffiths + input protein sequence stop site - + - - - - cDNA library - cDNA library lacks the non-coding and regulatory elements found in genomic DNA - A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription. - Dan Berrios - modified from Wikipedia - cDNA library + + + input gene sequence start site + When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence being analyzed is the input gene sequence start site. + + The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). + Emma Griffiths + input gene start + query gene start site + Emma Griffiths + input gene sequence start site - - - - - A categorical value specification in which the available categories were created with an explicit order. - https://en.wikipedia.org/wiki/Ordinal_data provides references for follow-up, but more than one OBI developer has objected to "...whose levels have natural, ordered categories and the distances between those categories is not known..." + -Separate from that, an OBI mechanism for asserting the order of ordinal values specification levels with OWL has not been determined yet. - Mark Andrew Miller, ORCID:0000-0001-9076-6066 - Bjoern Peters in https://github.com/obi-ontology/obi/issues/862 - https://github.com/obi-ontology/obi/issues/862 - ordinal value specification + + + input gene sequence stop site + When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence being analyzed is the input gene sequence stop site. + + The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). + Emma Griffiths + input gene stop + query gene stop site + Emma Griffiths + input gene sequence stop site - + - - - - - - - - - - - - - - - An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - rRNA-deleted RNA sequencing assay - PMID:29556074 - CFDE - ribosomal RNA-depleted RNA sequencing assay + + + reference protein sequence start site + When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being used for comparison is the reference protein sequence start site. + + The position of the first amino acid in a reference protein sequence (sequence being used for comparison). + Emma Griffiths + reference protein start + subject protein start site + Emma Griffiths + reference protein sequence start site - + - - - - - - - - - An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:31450270 - CFDE - metatranscriptome sequencing assay + + + reference protein sequence stop site + When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence used for comparison is the reference protein sequence stop site. + + The position of the last amino acid in a reference protein sequence (sequence being used for comparison). + Emma Griffiths + reference protein stop + subject protein stop site + Emma Griffiths + reference protein sequence stop site - + - - - An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - lipidomic assay - OBI metabolite profiling assay - CFDE - lipid profiling assay + + + reference gene sequence start site + When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence used for comparison is the reference gene sequence start site. + + The position of the first nucleotide in a reference gene sequence (sequence being used for comparison). + Emma Griffiths + reference gene start + subject gene start site + Emma Griffiths + reference gene sequence start site - + - - - snATAC-seq can be used to dissect heterogeneity and delineate gene regulatory sequences in complex tissues, and uncover both the cell types and the regulatory elements in each cell type without prior knowledge. - An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. - Mark Andrew Miller, ORCID:0000-0001-9076-6066 - snATAC-seq - http://www.biorxiv.org/content/early/2017/07/06/159137 - https://github.com/obi-ontology/obi/issues/864 - ENCODE - single-nucleus ATAC-seq + + + reference gene sequence stop site + When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence used for comparison is the reference gene sequence stop site. + + The position of the last nucelotide in a reference sequence (sequence being used for comparison). + Emma Griffiths + reference gene stop + subject gene stop site + Emma Griffiths + reference gene sequence stop site - + - - - - - - - - - - - - - - - - - - - - An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - 16S rRNA sequencing assay - PMID:31450270 - CFDE - 16s ribosomal gene sequencing assay + + + altitude measurement datum + + A length measurement datum between a point at sea or ground level and some point above it. + Chris Stoeckert + Adapted from https://www.merriam-webster.com/dictionary/altitude + altitude measurement datum - + - - - An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. - Mark Andrew Miller, ORCID:0000-0001-9076-6066 - scATAC-seq - http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html - https://github.com/obi-ontology/obi/issues/864 - ENCODE - single-cell ATAC-seq + + + capture Hi-C assay + PMID:29979818 Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. + + A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. + Bonita Lam + cHi-C + PMID:29979818 + https://github.com/obi-ontology/obi/issues/1251 + capture Hi-C assay - + - - + + @@ -69236,20 +85420,10 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s - + - - - - - - - - - - - - + + @@ -69257,60 +85431,27 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s - - - - - - - - - - - - - - - - - - - + - A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - metaproteomic assay - PMID:31450270 - CFDE - microbiome protein expression profiling assay - - - - - - - - - An analyte assay to study presence, concentration, or amount of cytokines. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:23603216 - CFDE - cytokine assay + magnetic resonance imaging assay + + An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. + Rebecca Jackson + MRI + url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging + https://github.com/obi-ontology/obi/issues/1290 + magnetic resonance imaging assay - + - - + + @@ -69322,7 +85463,7 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s - + @@ -69330,11 +85471,29 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s - + + computed tomography imaging assay + + An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity. + Rebecca Jackson + CAT scan + CT scan + computed tomography scan + url:https://www.mayoclinic.org/tests-procedures/ct-scan/about/pac-20393675 + https://github.com/obi-ontology/obi/issues/1290 + computed tomography imaging assay + + + + + + + + @@ -69343,10 +85502,10 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s - + - - + + @@ -69354,3813 +85513,5198 @@ Separate from that, an OBI mechanism for asserting the order of ordinal values s - - - - - - - - - - - + + + + + + positron emission tomography imaging assay + + An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. + Rebecca Jackson + PET scan + positron emission tomography scan + url:https://en.wikipedia.org/wiki/Positron_emission_tomography + https://github.com/obi-ontology/obi/issues/1290 + positron emission tomography imaging assay + + + + + + + + + duration of specimen collection + Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration. + + A time measurement datum that is the count of collection cycles over which a specimen collection process occurs. + specimen collection duration + VEuPathDB + specimen collection duration + + + + + + + + + + + + + + + + + + + + + + + + + material supplier + + A person or organization that provides material supplies to other people or organizations. + Rebecca Jackson + https://github.com/obi-ontology/obi/issues/1289 + material supplier + + + + + + + + + T cell receptor repertoire sequencing assay + + A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. + Rebecca Jackson + TCR repertoire sequencing assay + doi:10.1186/s12896-017-0379-9 + https://github.com/obi-ontology/obi/issues/1307 + T cell receptor repertoire sequencing assay + + + + + + + + + B cell receptor repertoire sequencing assay + + A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. + Rebecca Jackson + Antibody repertoire sequencing assay + BCR repertoire sequencing assay + doi:10.1186/s12896-017-0379-9 + https://github.com/obi-ontology/obi/issues/1307 + B cell receptor repertoire sequencing assay + + + + + + + + + prevalence of pathogen in specimens + prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR + + A data item that is the frequency of detection of a specified pathogenic organism in collected specimens. + Chris Stoeckert + prevalence of pathogen + VEuPathDB + prevalence of pathogen in specimens + + + + + + + + + prevalence of blood meal specimens from a host organism + prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal. + + A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens. + Chris Stoeckert + host blood index + VEuPathDB + prevalence of blood meal specimens from a host organism + + + + + + + + + presence of blood from host organism in blood meal specimen + presence of blood meal host organism indicated by boolean values of yes or no. + + A data item that indicates whether blood in a blood meal specimen came from a specified host organism. + Chris Stoeckert + presence of blood meal host organism + VEuPathDB + presence of blood from host organism in blood meal specimen + + + + + + + + + + + + + + - A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:29628929 - PMID:31450270 - CFDE - amplicon sequencing assay + blood meal source organism + + An organism that is the source of a blood meal. + Chris Stoeckert + blood meal host organism + VEuPathDB + blood meal source organism + + + + + + + + + blood meal source role + A mosquito feeds on a human whereby the human acquires the blood meal source role for the mosquito blood meal. + + A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism. + Will deprecate this term in VEuPathDB ontology once in OBI. + Chris Stoeckert + http://purl.obolibrary.org/obo/EUPATH_0000791 + blood meal source role + + + + + + + + + arthropod attractor role + + A role of a material entity realized in drawing an arthropod in the direction of the material. + John Judkins + attractant + IRO:0000034 + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + arthropod attractor role - + - - - A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - OBI:0002623 - CFDE - whole virome sequencing assay + + + arthropod collection process with automated identification + + An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + arthropod collection process with automated identification - + - - + + + gravid female arthropod specimen collection process - A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell. - Jie Zheng - EFO_0004426 karyotype - https://github.com/obi-ontology/obi/issues/1097 - VEuPathDB - karyotype information + An arthropod specimen collection process that has the objective of collecting gravid female arthropods. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + gravid female arthropod specimen collection process - + - - - - - - - - + + + resting flight-capable arthropod specimen collection process - A karyotype information that is about the structural variation of partial genome rather than whole genome. - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1097 - VEuPathDB - partial karyotype information + An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity. + John Judkins + VSMO:0000514 + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + resting flight-capable arthropod specimen collection process - + - - + + + daytime arthropod specimen collection by aspiration - A karyotype information that is about the structural variation of the whole genome. - Jie Zheng - OBI group - https://github.com/obi-ontology/obi/issues/1097 - full karyotype information + An arthropod specimen collection by aspiration that occurs in the daytime. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + daytime arthropod specimen collection by aspiration - + - - - An ordinal value specification that indicates that either -a) an analyte or mesaurand is present in an evaluant, or -b) that the amount of analyte/measurand detected is over some predetermined threshold. - Mark Andrew Miller, ORCID:0000-0001-9076-6066 - LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 32 - https://github.com/obi-ontology/obi/issues/1202 - bump - presence or over-threshold value specification + + + arthropod resting in human house specimen collection by aspiration + + An arthropod specimen collection by aspiration that catches specimens resting inside a human house. + John Judkins + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + arthropod resting in human house specimen collection by aspiration - + - - - Detection of SARS-CoV-2 IgG antibodies by an immunoassay method, such as enzyme-linked immunosorbent assay. This test is used in conjunction with SARS-CoV-2 IgA and IgM to aid in the diagnosis of COVID-19 and in the identification of individuals infected with SARS-CoV-2. - An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest - LOINC indicates that this class would not include flow cytometry or any technique that can determine the localization of an analyte, such as peroxidase immune staining or indirect immunofluorescence (IFA) - Mark Andrew Miller, ORCID:0000-0001-9076-6066 - IA - immunoassay - LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 47 - https://github.com/obi-ontology/obi/issues/1203 - single-value binding of antibody with reporter to antigen assay + + + landing arthropod specimen collection process + + An arthropod specimen collection process that occurs while the arthropods land on a surface. + John Judkins + collection of landing insects + VSMO:0001457 + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + landing arthropod specimen collection process - + - - - A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. - PERSON: Matthew Diller - platelet-poor plasma specimen + + + flying adult arthropod collection process by passive interception + + An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. + John Judkins + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + flying adult arthropod collection process by passive interception - + - - - A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm. - PERSON: Matthew Diller - platelet-poor plasma preparation process + + + device for collection of resting adult arthropods + + A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. + John Judkins + VSMO:0001355 + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + device for collection of resting adult arthropods - + - - - A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by an algorithm in order to quantify the frequency of different cell populations of interest. - Bjoern Peters - CMI-PB - https://github.com/obi-ontology/obi/issues/1226 - cytometry analysis by automated gating + + + well net for arthropod immatures + + A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. + John Judkins + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + well net for arthropod immatures - + - - - A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by a human operator in order to quantify the frequency of different cell populations of interest. - Bjoern Peters - CMI-PB - https://github.com/obi-ontology/obi/issues/1226 - cytometry analysis by manual gating + + + arthropod trap containing small non-human animal bait + + An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller. + John Judkins + trap containing small non-human animal bait + VSMO:0001595 + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + arthropod trap containing small non-human animal bait - + - - + + + trap for emerging adult arthropods + + An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage. + John Judkins + American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389 + VSMO:0001352 + https://github.com/obi-ontology/obi/issues/1302 + VEuPathDB + trap for emerging adult arthropods + + + + + + + + - + - + - - - - - - - - - + + + + - - A specimen that is collected with a suctioning tube from the trachea. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - tracheal wash specimen - PMID:25338241 - tracheal aspirate specimen + + ferritin assay + + An assay that measures ferritin + James A. Overton, ORCID:0000-0001-5139-5557 + OBI + ferritin assay - + - + - - - + + + + - - - - - - - - - - - - + + - - + + - A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 - mid-turbinate nasal swab specimen + fibrinogen assay + + An assay that measures fibrinogen + James A. Overton, ORCID:0000-0001-5139-5558 + OBI + fibrinogen assay - + - + + - - + - + - - + + + + + + - A specimen that is collected with a suctioning tube from the nasal cavity. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - nasal wash specimen|nasopharyngeal aspirate - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - nasal aspirate specimen + iron assay + + An analyte assay that measures the abundance of iron + James A. Overton, ORCID:0000-0001-5139-5559 + OBI + iron assay - + - + + - - + - + - - + + + + + + - A specimen that is collected with a suctioning tube from the lower respiratory tract. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - lower respiratory tract wash specimen - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - lower respiratory tract aspirate specimen + ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium + James A. Overton, ORCID:0000-0001-5139-5561 + OBI + ionized calcium assay - + - + + - - + - + - - + + + + + + - A specimen that is derived from the upper respiratory tract - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - upper respiratory specimen + transferrin assay + + An analyte assay that measures the abundance of transferrin + James A. Overton, ORCID:0000-0001-5139-5562 + OBI + transferrin assay - + - + + - - + - + - - + + + + + + - A specimen that is derived from the lower respiratory tract. - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - lower respiratory tract specimen + uric acid assay + + An analyte assay that measures the abundance of uric acid + James A. Overton, ORCID:0000-0001-5139-5563 + OBI + uric acid assay - + - + + - - + - + - - + + + + + + - A specimen that is derived from the anterior nasal wall - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - Asiyah Yu Lin ORCID:0000-0003-2620-0345 - anterior nasal swab specimen + globulin assay + + An analyte assay that measures the abundance of globulin + James A. Overton, ORCID:0000-0001-5139-5564 + OBI + globulin assay - + - - - Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 - aspiration procedure - https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C15631 - aspiration specimen collection + + + + + + + + + + + + + + + + + + myelocyte assay + + A cytometry assay that measures the abundance and/or characteristics of myelocytes + James A. Overton, ORCID:0000-0001-5139-5565 + OBI + myelocyte assay - + - - - personal protective device - Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. - PPE is equipment worn by a worker to minimize exposure to specific hazards. - - A device which is a wearable garment designed to protect the wearer's body from injury or infection. - https://orcid.org/0000-0002-8844-9165 - PPE - personal protective equipment - https://en.wikipedia.org/wiki/Personal_protective_equipment - https://github.com/obi-ontology/obi/issues/1193 - personal protective device + + + + + + + + + + + + + + + + + + metamyelocyte assay + + A cytometry assay that measures the abundance and/or characteristics of metamyelocytes + James A. Overton, ORCID:0000-0001-5139-5566 + OBI + metamyelocyte assay - + - - - face mask - A systematic review on the efficacy of face coverings against respiratory viruses analyzed 19 randomized trials and concluded that use of face masks and respirators appeared to be protective in both health care and community settings - - A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles. - https://orcid.org/0000-0002-8844-9165 - face covering - respirator - Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask - https://github.com/obi-ontology/obi/issues/1193 - face mask + + + + + + + + + + + + + + + + + + hematocrit assay + + A cytometry assay that measures the proportion of red blood cells + James A. Overton, ORCID:0000-0001-5139-5567 + OBI + hematocrit assay - + - - - non-medical mask - A non-medical mask may contain fabrics that are not regulated for use in surgical masks or respirators, or may not be designed to form a seal around the nose and mouth. - - A face mask not manufactured according to medical equipment standards. - https://orcid.org/0000-0002-8844-9165 - cloth mask - https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html - https://github.com/obi-ontology/obi/issues/1193 - non-medical mask + + + + + + + + + + + + + + + + + + promyelocyte assay + + A cytometry assay that measures the abundance and/or characteristics of promyelocytes + James A. Overton, ORCID:0000-0001-5139-5568 + OBI + promyelocyte assay - + - - - medical mask - The finding of a much higher rate of infection in the cloth mask arm could be interpreted as harm caused by cloth masks, efficacy of medical masks, or most likely a combination of both. - - A face mask manufactured according to a recognized medical equipment standard. - https://orcid.org/0000-0002-9578-0788 - surgical mask - https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html - https://github.com/obi-ontology/obi/issues/1193 - medical mask + + + + + + + + + + + + + + + + + + basophil assay + + A cytometry assay that measures the abundance and/or characteristics of basophils + James A. Overton, ORCID:0000-0001-5139-5569 + OBI + basophil assay + + + + + + + + + + + + + + + + + + + + + + + + neutrophil assay + + A cytometry assay that measures the abundance and/or characteristics of neutrophils + James A. Overton, ORCID:0000-0001-5139-5570 + OBI + neutrophil assay + + + + + + + + + + + + + + + + + + + + + + + + eosinophil assay + + A cytometry assay that measures the abundance and/or characteristics of eosinophils + James A. Overton, ORCID:0000-0001-5139-5571 + OBI + eosinophil assay + + + + + + + + + + + + + + + + + + + + + + + + lymphocyte assay + + A cytometry assay that measures the abundance and/or characteristics of lymphocytes + James A. Overton, ORCID:0000-0001-5139-5572 + OBI + lymphocyte assay - + - - - N95 respirator - - A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles. - https://orcid.org/0000-0002-8844-9165 - N95 - N95 face mask - N95 facemask - N95 respirator mask - https://en.wikipedia.org/wiki/N95_mask - https://github.com/obi-ontology/obi/issues/1193 - N95 respirator + + + + + + + + + + + + + + + + + + monocyte assay + + A cytometry assay that measures the abundance and/or characteristics of monocytes + James A. Overton, ORCID:0000-0001-5139-5573 + OBI + monocyte assay - + - - - face shield - - A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials. - https://orcid.org/0000-0002-8844-9165 - faceshield - splash shield - https://en.wikipedia.org/wiki/Face_shield - https://github.com/obi-ontology/obi/issues/1193 - face shield + + + + + + + + + + + + + + + + + + reticulocyte assay + + A cytometry assay that measures the abundance and/or characteristics of reticulocytes + James A. Overton, ORCID:0000-0001-5139-5574 + OBI + reticulocyte assay - + - - - patient gown - - A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff. - https://orcid.org/0000-0002-8844-9165 - hospital gown - https://en.wikipedia.org/wiki/Patient_gown - https://github.com/obi-ontology/obi/issues/1193 - patient gown + + + + + + + + + + + + + + + + + + macrophage assay + + A cytometry assay that measures the abundance and/or characteristics of macrophages + James A. Overton, ORCID:0000-0001-5139-5577 + OBI + macrophage assay - + - - - scrubs - Examples consist of a short-sleeve V-necked shirt and drawstring pants or a short-sleeve calf-length dress, a tie-back or bouffant-style cap, a mask, a surgical gown, latex gloves, and supportive closed-toe shoes. - - A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap. - https://orcid.org/0000-0002-8844-9165 - scrub clothing item - https://en.wikipedia.org/wiki/Scrubs_(clothing) - https://github.com/obi-ontology/obi/issues/1193 - scrubs + + + + + + + + + + + + + + + + + + platelet assay + + A cytometry assay that measures the abundance and/or characteristics of platelets + James A. Overton, ORCID:0000-0001-5139-5578 + OBI + platelet assay - + - - - reusable patient gown - - A patient gown intended to be reused after being laundered. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Patient_gown - https://github.com/obi-ontology/obi/issues/1193 - reusable patient gown + + + + + + + + + barcode target locus role + + An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. + Chris Stoeckert https://orcid.org/0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1325 + barcode target locus role - + - - - disposable patient gown - - A patient gown intended for a single period of continuous use and then disposed of. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Patient_gown - https://github.com/obi-ontology/obi/issues/1193 - disposable patient gown + + + + + + + + + oligonucleotide primer set + + A processed material that consists of oligonucleotides that bear a primer role. + Chris Stoeckert https://orcid.org/0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1325 + oligonucleotide primer set - + - - - medical gown - - A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional. - https://orcid.org/0000-0002-8844-9165 - hospital gown - https://en.wikipedia.org/wiki/Medical_gown - https://github.com/obi-ontology/obi/issues/1193 - medical gown + + + fluorogenic PCR assay + + A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. + John Judkins + TaqMan + MIRO:20000102 + https://github.com/obi-ontology/obi/issues/1320 + fluorogenic PCR assay - + - - - apron - - A garment which is worn over other clothing and covers mainly the front of the body. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Apron - https://github.com/obi-ontology/obi/issues/1193 - apron + + + + + + + + + genotyping by PCR assay + genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci. + + A genotyping assay that uses polymerase chain reaction. + Chris Stoeckert, ORCID:0000-0002-5714-991X + Jie Zheng, ORCID:0000-0002-2999-0103 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1348 + VEuPathDB + genotyping by PCR assay - + - - - surgical gown - - A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - surgical gown + + + cleavage under targets and release using nuclease assay + + A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CUT&RUN assay + url:https://elifesciences.org/articles/21856 + https://github.com/obi-ontology/obi/issues/1192 + bonitalam + cleavage under targets and release using nuclease assay - + - - - personal protective glove - - A personal protective device which is a glove. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - personal protective glove + + + cleavage under targets and tagmentation + + A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CUT&Tag assay + url:https://www.nature.com/articles/s41467-019-09982-5 + https://github.com/obi-ontology/obi/issues/1192 + bonitalam + cleavage under targets and tagmentation - + - - - personal protective clothing item - - A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - personal protective clothing item + + + coma severity assay + Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. + + A physical examination of individual that has the objective to determine the severity of coma in a patient. + John Judkins + https://github.com/obi-ontology/obi/issues/1357 + John Judkins + coma severity assay - + - - - laboratory coat - - A personal protective clothing item which is an overcoat worn by medical or laboratory professionals. - https://orcid.org/0000-0002-8844-9165 - white coat - https://en.wikipedia.org/wiki/White_coat - https://github.com/obi-ontology/obi/issues/1193 - laboratory coat + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Plasmodium gametocyte detection assay + + An assay that detects Plasmodium gametocytes in a specimen. + Chris Stoeckert + Jie Zheng + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + Plasmodium gametocyte detection assay - + - - - medical glove - - A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Medical_glove - https://github.com/obi-ontology/obi/issues/1193 - medical glove + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + malaria rapid diagnosis assay + + An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. + Chris Stoeckert + Jie Zheng + malaria rapid diagnosis test + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + malaria rapid diagnosis assay - + - - - nitrile glove - - A personal protective glove which is made out of nitrile rubber. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Medical_glove - https://github.com/obi-ontology/obi/issues/1193 - nitrile glove + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + parasite detection assay + + An assay that detects parasite in a specimen. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite detection assay - + - - - transparent partition - - A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. - https://orcid.org/0000-0002-8844-9165 - transparent partition - https://ncceh.ca/content/blog/physical-barriers-covid-19-infection-prevention-and-control-commercial-settings - https://github.com/obi-ontology/obi/issues/1193 - transparent droplet barrier + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + feces microbiology assay + + An assay that detects microorganisms in a feces specimen. + John Judkins + stool test for microorganisms + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + feces microbiology assay - + - - - footwear cover - - A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants. - https://orcid.org/0000-0002-8844-9165 - boot cover - shoe cover - https://en.wiktionary.org/wiki/shoecover - https://github.com/obi-ontology/obi/issues/1193 - footwear cover + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood assay + + An assay that has a blood specimen as evaulant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + blood assay - + - - - disposable footwear cover - - A footwear cover which is designed for a single period of continuous use and then disposed of. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - disposable footwear cover + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + falcivax rapid diagnostic test + + A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + falcivax rapid diagnostic test - + - - - reusable footwear cover - - A footwear cover which is designed for repeated use. - https://orcid.org/0000-0002-8844-9165 - OBI - https://github.com/obi-ontology/obi/issues/1193 - reusable footwear cover + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + optimal-IT rapid diagnostic test + + A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + optimal-IT rapid diagnostic test - + - - - surgical N95 respirator - - A N95 respirator which has been approved by the FDA as a surgical mask. - https://orcid.org/0000-0002-8844-9165 - healthcare respirator - medical respirator - surgical N95 - surgical N95 respirator - https://multimedia.3m.com/mws/media/1794572O/surgical-n95-vs-standard-n95-which-to-consider.pdf - https://github.com/obi-ontology/obi/issues/1193 - surgical N95 respirator + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine assay + + An assay that has a urine specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + urine assay - + - - - protective coverall - - A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination. - https://orcid.org/0000-0002-8844-9165 - https://www.safeopedia.com/definition/863/disposable-coveralls - https://github.com/obi-ontology/obi/issues/1193 - protective coverall + + + + + + + + + + + + + + + + parasite species identification by PCR assay + + An organism identification assay that identifies the species of parasites by PCR. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite species identification by PCR assay - + - - - protective sleeve - A protective sleeve can be designed to provide protection from heat, welding spatter or hot metal, chemicals, sharp objects, paint or other liquids. - - A personal protective clothing item which is a protective cover worn over the arm. - https://orcid.org/0000-0002-8844-9165 - https://www.safeopedia.com/definition/974/protective-sleeves - https://github.com/obi-ontology/obi/issues/1193 - protective sleeve + + + + + + + + + + + + + + + + + + + + + + parasite detection by PCR assay + + An assay that detects parasite in a specimen using PCR. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite detection by PCR assay - + - - - protective apron - - A personal protective clothing item which is an apron. - https://orcid.org/0000-0002-8844-9165 - https://en.wikipedia.org/wiki/Apron - https://github.com/obi-ontology/obi/issues/1193 - protective apron + + + free-standing window trap + Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658] + + An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die. + VEuPathDB + VSMO:0001649 + free-standing window trap - + - - - medical cap - - A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp. - https://orcid.org/0000-0002-8844-9165 - bouffant cap - bouffant hat - medical bonnet - scrub cap - surgical hat - https://en.wikipedia.org/wiki/Scrubs_(clothing) - https://github.com/obi-ontology/obi/issues/1193 - medical cap + + + + + + + + + BG-lure scent dispenser + + A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin. + VEuPathDB + BG-lure + IRO:0001060 + BG-lure scent dispenser - + - + - specimen collection device - - A container used to collect a specimen. - https://orcid.org/0000-0002-8844-9165 - specimen collection device + hand-held sweep net + + A device that consists of a network of mesh and is designed to capture adult arthropods. + VEuPathDB + VSMO:0001522 + hand-held sweep net - + - - - chromatography vial + + + Centers for Disease Control and Prevention gravid trap + The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658] - A vial with cap and container material suited to optical, sanitary and handling requirements of chromatography. - PERSON:Daniel Schober - GROUP:<http://msi-ontology.sourceforge.net> - http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 - chromatography vial + A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan. + VEuPathDB + CDC gravid trap + VSMO:0001510 + Centers for Disease Control and Prevention gravid trap - + - - - specimen pad - An absorbent pad and its accompanying container are designed to provide safe storage and transport to various degrees for diagnostic and clinical samples, infectious and hazardous materials, chemicals, pharmaceuticals and environmental samples. - - A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter. - https://orcid.org/0000-0002-8844-9165 - absorbant pad - polysponge - sample pad - sampling sponge - specimen sponge - surface wipe - swab - Derived from NCIT sponge definition. - specimen pad + + + egg specimen collection process + + An arthropod specimen collection process in which the arthropods are in the embryo stage. + VEuPath + collection of eggs + MIRO:30000049 + https://github.com/obi-ontology/obi/issues/1322 + egg specimen collection process - + - - - specimen collection swab stick - A swab stick allows a worker to collect samples without touching the inside of the bag - - A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material. - https://orcid.org/0000-0002-8844-9165 - polyprobe - sponge probe - sponge stick - sponge-stick - https://medical-dictionary.thefreedictionary.com/swab - specimen collection swab stick + + + larval specimen collection process + + An arthropod specimen collection process in which the arthropods are in the larval stage. + VEuPath + collection of larvae + MIRO:30000022 + https://github.com/obi-ontology/obi/issues/1322 + larval specimen collection process - + - - - cotton swab - - A device which is a cotton pad mounted on one or both ends of a stick. - https://orcid.org/0000-0002-8844-9165 - Q-tip - swab-sampler - https://en.wikipedia.org/wiki/Cotton_swab - cotton swab + + + pupal specimen collection process + + An arthropod specimen collection process in which the arthropods are in the pupal stage. + VEuPath + collection of pupae + MIRO:30000050 + https://github.com/obi-ontology/obi/issues/1322 + pupal specimen collection process - + - - + - - - - + + + + + + + + + + + + + - drag swab - - A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string - https://orcid.org/0000-0002-8844-9165 - https://www.fda.gov/food/laboratory-methods-food/environmental-sampling-and-detection-salmonella-poultry-houses - drag swab + blood specimen in vacutainer + + A blood specimen that is located in a vacutainer. + John Judkins + Vacutainer sample + VEuPathDB + blood specimen in vacutainer - + - - - pre-moistened swab stick - - A specimen collection swab stick that is pre-moistened with liquid prior to sampling. - https://orcid.org/0000-0002-8844-9165 - pre-moistened swab stick + + + + + + + + + + + + + + + + + blood specimen on filter paper + + A blood specimen that is located on a filter paper. + Chris Stoeckert + Jie Zheng + Filter paper sample + Penn Group + blood specimen on filter paper - + - - - surface wipe - Surface sampling procedures involved the use of polyester wipes, swabs, contact slides (two types), and adhesive tapes; a gelatin filter was used to sample the air. - - A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces. - https://orcid.org/0000-0002-8844-9165 - https://www.science.gov/topicpages/s/surface+wipe+sampling.html - surface wipe + + + proportion mapped reads + + A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads. + John Judkins + VEuPathDB + proportion mapped reads - + - - - catheter - A catheter left inside the body, either temporarily or permanently, may be referred to as an "indwelling catheter". - - A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body. - https://orcid.org/0000-0002-8844-9165 - http://purl.bioontology.org/ontology/MESH/D057785 - catheter + + + + + + + + + + + + + + + + + + + antibiotic administration process + + Administering substance in vivo where an antibiotic substance is administered to a living organism. + Chris Stoeckert + Cristian Cocos + Jie Zheng + Penn Group + antibiotic administration process - + - - - surveillance process - An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. - Chris Stoeckert - Shane Babcock, OBI - https://github.com/obi-ontology/obi/issues/1181 - IDO, VEuPathDB - surveillance process + + + insecticide resistance datum + + A data item that is about resistance to an insecticide. + John Judkins + VEuPathDB + insecticide resistance datum - + - - - cluster study group role - A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound. - A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. - Chris Stoeckert, Brianna Lindsay - cluster study arm - ClinEpiDB - cluster study group role + + + organism identification datum + + A data item that is the specified output of an organism identification assay. + John Judkins + VEuPathDB + organism identification datum - + - - - compound study group role - A compound study group consisting of geographically proximate households that share a common water source. - A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. - Chris Stoeckert, Brianna Lindsay - compound study arm - ClinEpiDB - compound study group role + + + easting coordinate measurement datum + + A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. + Easting and northing coordinates are commonly measured in meters from a horizontal datum. + John Judkins + https://en.wikipedia.org/wiki/Grid_reference_system + easting coordinate measurement datum - + - - - ultraviolet light source - - A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. - Person: Jie Zheng - UV light source - Person: Jie Zheng - https://github.com/obi-ontology/obi/issues/1200 - VEuPathDB - ultraviolet light source + + + northing coordinate measurement datum + + A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. + Easting and northing coordinates are commonly measured in meters from a horizontal datum. + John Judkins + https://en.wikipedia.org/wiki/Grid_reference_system + northing coordinate measurement datum - + - - - visible light source - - A light source that provides visible light for use in a distant area using a delivery system. - Person: Jie Zheng - Person: Jie Zheng - https://github.com/obi-ontology/obi/issues/1200 - VEuPathDB - visible light source + + + clinical study center + + Organization that undertakes a clinical study at some point in time. + Chris Stoeckert + Cristian Cocos + Jie Zheng + Penn Group + clinical study center - + - - - solar light source - - A light source that light is produced from solar energy. - Person: Chris Stoeckert - Person: Jie Zheng - Person: Chris Stoeckert - Person: Jie Zheng - https://github.com/obi-ontology/obi/issues/1200 - VEuPathDB - solar light source + + + sequencing protocol + + A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. + John Judkins + VEuPathDB + sequencing protocol - + - - - A live arthropod specimen collection process in which the arthropods are in the adult stage. - John Judkins - collection of adults - MIRO:30000052 - https://github.com/obi-ontology/obi/issues/1217 - adult arthropod specimen collection process + + + + + + + + + specimen collection protocol + + A protocol that specifies processes to fulfill a specimen collection objective. + John Judkins + VEuPathDB + specimen collection protocol - + - - - An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. - John Judkins - animal biting catch - MIRO:30000012 - https://github.com/obi-ontology/obi/issues/1217 - animal-biting arthropod specimen collection by aspiration + + + + + + + + + + + + + + + + + + + participant identifier + + A symbol that denotes a participant under investigation. + John Judkins + VEuPathDB + participant identifier - + - - - An animal-biting arthropod specimen collection by aspiration that occurs outside a building. - John Judkins - animal biting catch - outdoors - MIRO:30000014 - https://github.com/obi-ontology/obi/issues/1217 - animal-biting outdoor arthropod specimen collection by aspiration + + + axillary temperature measurement datum + + A temperature measurement datum that is about an axilla. + John Judkins + VEuPathDB + axillary temperature measurement datum - + - - - An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. - John Judkins - aquatic environment catch - MIRO:30000048 - https://github.com/obi-ontology/obi/issues/1217 - aquatic arthropod specimen collection process + + + organismal body temperature measurement datum + + A temperature measurement datum that is about an organism. + Chris Stoeckert + Jie Zheng + Penn Group + organismal body temperature measurement datum - + - - - An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. - John Judkins - animal shed resting catch - MIRO:30000027 - https://github.com/obi-ontology/obi/issues/1217 - arthropod resting in animal house specimen collection by aspiration + + + + + + + + + common name of organism + + A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized. + John Judkins + https://en.wikipedia.org/wiki/Common_name + common name of organism - + - - - An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture. - John Judkins - outdoors shelter catch - artificial - MIRO:30000026 - https://github.com/obi-ontology/obi/issues/1217 - arthropod resting outdoors on artificial support specimen collection by aspiration + + + age since birth at time of enrollment + + An age since birth measurement datum at the time of subject enrollment. + Jie Zheng + Penn Group + age since birth at time of enrollment - + - - - An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant. - John Judkins - outdoors shelter catch - natural - MIRO:30000025 - https://github.com/obi-ontology/obi/issues/1217 - arthropod resting outdoors on natural support specimen collection by aspiration + + + age since birth at time of visit + + An age since birth measurement datum at the time of a clinical visit. + Chris Stoeckert + Grant Dorsey + Jie Zheng + Shon Cade + Penn Group + age since birth at time of visit - + - - - An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity. - John Judkins - outdoors shelter catch - MIRO:30000024 - https://github.com/obi-ontology/obi/issues/1217 - arthropod resting outdoors specimen collection by aspiration + + + entomological data item + + A data item that is about a collection of insects. + John Judkins + entomological measurement datum + VEuPathDB + entomological data item - + - - - A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container. - John Judkins - catch by aspiration - MIRO:30000043 - https://github.com/obi-ontology/obi/issues/1217 - arthropod specimen collection by aspiration + + + temperature measurement datum + + A scalar measurement datum that is the result of measuring temperature. + John Judkins + VEuPathDB + temperature measurement datum - + - - - A specimen collection process that has the objective of collecting arthropods as specimens. - John Judkins - collection of arthropods - field population catch - MIRO:30000044 - https://github.com/obi-ontology/obi/issues/1217 - arthropod specimen collection process + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organismal body temperature measurement assay + + An assay that detects body temperature of an organism. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + organismal body temperature measurement assay - + - - - An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. - John Judkins - man biting catch - MIRO:30000017 - https://github.com/obi-ontology/obi/issues/1217 - human-biting arthropod specimen collection by aspiration + + + extraction date + + A time measurement datum that specifies when some material was extracted from an input material. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + FLU, VEuPathDB + https://github.com/obi-ontology/obi/issues/1286 + extraction date - + - - - An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. - John Judkins - man biting catch - indoors - MIRO:30000019 - https://github.com/obi-ontology/obi/issues/1217 - human-biting indoor arthropod specimen collection by aspiration + + + extraction duration time + + A time measurement datum that is the result of measuring the duration of an extraction process. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + Meredith Keybl, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + extraction duration time - + - - - An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building. - John Judkins - man biting catch - outdoors - MIRO:30000018 - https://github.com/obi-ontology/obi/issues/1217 - human-biting outdoor arthropod specimen collection by aspiration + + + specimen collection time post disease onset + + A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + GROUP:FLU, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + specimen collection time post disease onset - + - - - A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. - John Judkins - pyrethrum spray catch - MIRO:30000023 - https://github.com/obi-ontology/obi/issues/1217 - knockdown arthropod specimen collection by pyrethrum spray + + + specimen collection time post infection + + A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + VEuPathDB, EUPATH:0000613 + https://github.com/obi-ontology/obi/issues/1286 + specimen collection time post infection - + - - - An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. - John Judkins - knockdown collection - IRO:0000014 - https://github.com/obi-ontology/obi/issues/1217 - knockdown arthropod specimen collection process + + + laboratory postal address + + A postal address used as a directive to deliver something to a laboratory. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + laboratory address + GROUP:FLU, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + laboratory postal address - + - - - An arthropod specimen collection process meant to collect live specimens. - John Judkins - catch of live specimens - MIRO:30000044 - VSMO:0001445 - https://github.com/obi-ontology/obi/issues/1217 - live arthropod specimen collection process + + + laboratory-based population + Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033) + + A population where the collection of individuals is located and maintained in a laboratory, research, or production facility. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1370 + laboratory-based population - + - - - A device designed to catch arthropods. - John Judkins - MIRO:30000011 - https://github.com/obi-ontology/obi/issues/1217 - arthropod trap + + + autofluorescence assay + + A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + intrinsic fluorescence assay + PMID:25578980 + url:https://en.wikipedia.org/wiki/Autofluorescence + https://github.com/obi-ontology/obi/issues/1393 + CFDE + autofluorescence assay - + - - - An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected. - John Judkins - IRO:0000005 - https://github.com/obi-ontology/obi/issues/1217 - artificial pit shelter + + + + + + + + + + + + + + + + + + + + + + + + + + + autofluorescence microscopy assay + + An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:25578980 + url:https://en.wikipedia.org/wiki/Autofluorescence + https://github.com/obi-ontology/obi/issues/1394 + CFDE + autofluorescence microscopy assay - + - - - An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal. - John Judkins - https://github.com/obi-ontology/obi/issues/1217 - baited net trap + + + bulk assay for transposase-accessible chromatin using sequencing + + An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + bulk ATAC-seq + PMID:24097267 + https://github.com/obi-ontology/obi/issues/1395 + CFDE + bulk assay for transposase-accessible chromatin using sequencing - + - - - An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. - John Judkins - IRO:0000017 - https://github.com/obi-ontology/obi/issues/1217 - barrier trap + + + bulk RNA-seq assay + + An RNA-seq assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.biostars.org/p/458516/ + https://github.com/obi-ontology/obi/issues/1396 + CFDE + bulk RNA-seq assay - + - - + + - - + + + + + + + + + - A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. - John Judkins - IRO:0000143 - https://github.com/obi-ontology/obi/issues/1217 - BG-Counter + multiplexed fluorescent antibody imaging assay + + An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:29993362 + https://github.com/obi-ontology/obi/issues/1397 + CFDE + multiplexed fluorescent antibody imaging assay - + - - - - - - - - - An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current. - John Judkins - IRO:0000028 - VSMO:0001906 - https://github.com/obi-ontology/obi/issues/1217 - BG-Sentinel trap + + + Cell DIVE multiplexed imaging assay + + A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://cancerres.aacrjournals.org/content/80/16_Supplement/1448 + url:https://www.cytivalifesciences.co.kr/wp-content/uploads/2020/07/Cell-DIVE-Tech-Info-Sheet-CY11898-09Apr20-DF.pdf + https://github.com/obi-ontology/obi/issues/1398 + CFDE + Cell DIVE multiplexed imaging assay - + - - - A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery. - This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. - John Judkins - CDC light trap - IRO:0000163 - https://github.com/obi-ontology/obi/issues/1217 - Centers for Disease Control and Prevention light trap + + + co-detection by indexing assay + + A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CODEX + url:https://www.scilifelab.se/facilities/co-detection-by-indexing-codex/ + https://github.com/obi-ontology/obi/issues/1399 + CFDE + co-detection by indexing assay - + - - - A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. - John Judkins - dipper for immatures - VSMO:0001479 - https://github.com/obi-ontology/obi/issues/1217 - dipper for arthropod immatures + + + + + + + + + + + + + + + + fluorescence in-situ hybridization assay + + An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + FISH + url:https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization + https://github.com/obi-ontology/obi/issues/1400 + CFDE + fluorescence in-situ hybridization assay - + - - - A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods. - John Judkins - EVS trap - IRO:0000029 - VSMO:0001295 - https://github.com/obi-ontology/obi/issues/1217 - encephalitis virus surveillance trap + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + decoding amplified targeted transcripts with fluorescence in situ hybridization assay + + A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + DARTFISH + url:http://genome-tech.ucsd.edu/ZhangLab/index.php/data/tech-dev/ + url:http://www.weizmann.ac.il/conferences/SCG2015/sites/conferences.SCG2015/files/scg_2015_abstractbook_online_version.pdf + url:https://escholarship.org/uc/item/5bq3128f + https://github.com/obi-ontology/obi/issues/1401 + CFDE + decoding amplified targeted transcripts with fluorescence in situ hybridization assay - + - - - An arthropod trap that is designed to collect gravid female arthropods or their eggs. - John Judkins - IRO:0000030 - https://github.com/obi-ontology/obi/issues/1217 - gravid trap + + + imaging mass cytometry assay + + A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + IMC + imaging CyTOF + PMID:31798587 + https://github.com/obi-ontology/obi/issues/1403 + CFDE + imaging mass cytometry assay - + - - - An arthropod trap that uses light as an attractant. - John Judkins - MIRO:30000065 - https://github.com/obi-ontology/obi/issues/1217 - light trap + + + + + + + + + + + + + + + + + + + + + + + + + + + liquid chromatography mass spectrometry assay + + A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + LC-MS + CHMO:0000524 + https://github.com/obi-ontology/obi/issues/1404 + CFDE + liquid chromatography mass spectrometry assay - + - - - A light trap designed to be placed inside a building. - John Judkins - indoor light trap - MIRO:30000009 - https://github.com/obi-ontology/obi/issues/1217 - light trap for indoor use + + + lightsheet fluorescence microscopy assay + + A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/light-sheet-fluorescence-microscopy + https://github.com/obi-ontology/obi/issues/1405 + CFDE + lightsheet fluorescence microscopy assay - + - - - A light trap designed to be placed outside a building. - John Judkins - outdoor light trap - MIRO:30000010 - https://github.com/obi-ontology/obi/issues/1217 - light trap for outdoor use + + + matrix assisted laser desorption ionization imaging mass spectrometry assay + + A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + MALDI-IMS + url:http://purl.obolibrary.org/obo/CHMO_0000054 + https://github.com/obi-ontology/obi/issues/1406 + CFDE + matrix assisted laser desorption ionization imaging mass spectrometry assay - + - - - An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. - John Judkins - IRO:0000022 - https://github.com/obi-ontology/obi/issues/1217 - Mosquito Magnet trap + + + multiplexed ion beam imaging assay + + A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + MIBI + url:https://www.nature.com/articles/s41374-020-0417-4 + https://github.com/obi-ontology/obi/issues/1407 + CFDE + multiplexed ion beam imaging assay - + - - - A gravid trap consisting of an arthropod attractant and adhesive surface. - John Judkins - IRO:0000140 - https://github.com/obi-ontology/obi/issues/1217 - MosquiTRAP + + + nanospray desorption electrospray ionization assay + + A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + NanoDESI + url:https://pubmed.ncbi.nlm.nih.gov/20593081/ + https://github.com/obi-ontology/obi/issues/1408 + CFDE + nanospray desorption electrospray ionization assay - + - - - A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. - John Judkins - New Jersey trap - IRO:0000031 - https://github.com/obi-ontology/obi/issues/1217 - New Jersey light trap + + + + + + + + + + + + + + + + nanodroplet processing in one pot for trace samples assay + + A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + NanoPOTS + url:https://www.emsl.pnnl.gov/science/related-instrument/nanodroplet-processing-in-one-pot-for-trace-samples--nanopots-/1806 + https://github.com/obi-ontology/obi/issues/1409 + CFDE + nanodroplet processing in one pot for trace samples assay - + - - - A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter. - John Judkins - OVI light-suction trap - IRO:0000154 - Parasites Vectors 8, 239 (2015) - https://github.com/obi-ontology/obi/issues/1217 - Onderstepoort Veterinary Institute light-suction trap + + + periodic acid-Schiff staining assay + + A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PAS staining + url:https://microbenotes.com/periodic-acid-schiff-pas-staining/ + https://github.com/obi-ontology/obi/issues/1410 + CFDE + periodic acid-Schiff staining assay - + - - - An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. - John Judkins - outlet window trap - MIRO:30000020 - https://github.com/obi-ontology/obi/issues/1217 - outlet window trap + + + single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing + + An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + sciATACseq + url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158300/ + https://github.com/obi-ontology/obi/issues/1411 + CFDE + single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing - + - - - An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females. - John Judkins - oviposition trap - MIRO:30000016 - VSMO:0001501 - https://github.com/obi-ontology/obi/issues/1217 - ovitrap + + + single-cell combinatorial indexing RNA sequencing assay + + A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + sciRNAseq + url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894354/ + https://github.com/obi-ontology/obi/issues/1412 + CFDE + single-cell combinatorial indexing RNA sequencing assay - + - - - An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. - John Judkins - https://github.com/obi-ontology/obi/issues/1217 - resting arthropod trap + + + sequential fluorescence in-situ hybridization assay + + A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + seqFISH + url:https://spatial.caltech.edu/seqfish/ + https://github.com/obi-ontology/obi/issues/1413 + CFDE + sequential fluorescence in-situ hybridization assay - + - - - An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. - John Judkins - resting box catch - IRO:0000021 - https://github.com/obi-ontology/obi/issues/1217 - resting box trap + + + slide-seq assay + + An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://science.sciencemag.org/content/363/6434/1463 + https://github.com/obi-ontology/obi/issues/1414 + CFDE + slide-seq assay - + - - - An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host). - John Judkins - resting bucket catch - IRO:0000141 - https://github.com/obi-ontology/obi/issues/1217 - resting bucket + + + single-nucleus chromatin accessibility and mRNA expression sequencing assay + + A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + SNARE-seq + SNAREseq + url:https://www.nature.com/articles/s41587-019-0290-0 + https://github.com/obi-ontology/obi/issues/1416 + CFDE + single-nucleus chromatin accessibility and mRNA expression sequencing assay - + - - - An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap. - John Judkins - shannon trap catch - IRO:0000191 - https://github.com/obi-ontology/obi/issues/1217 - Shannon trap + + + single-nucleus RNA sequencing assay + + A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + sNuc-seq + single nuclei RNA sequencing + snRNA-seq + EFO:0009809 + url:https://www.biocompare.com/Editorial-Articles/557506-Advantages-of-Single-Nucleus-RNA-Sequencing/ + https://github.com/obi-ontology/obi/issues/1415 + CFDE + single-nucleus RNA sequencing assay - + - - - An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected. - John Judkins - sticky resting bucket catch - IRO:0000142 - https://github.com/obi-ontology/obi/issues/1217 - sticky resting bucket + + + gas chromatography mass spectrometry assay + + A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + GC-MS + url:http://purl.bioontology.org/ontology/MESH/D008401 + https://github.com/obi-ontology/obi/issues/1417 + CFDE + gas chromatography mass spectrometry assay - + - - - An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. - John Judkins - sticky trap catch - IRO:0000128 - https://github.com/obi-ontology/obi/issues/1217 - sticky trap + + + SOMAscan assay + + An analyte assay that uses aptamers to detect protein analytes in serum. + Bjoern Peters + Randi Vita + Rohloff JC, et al. Nucleic acid ligands with protein-like side chains: modified aptamers and their uses as diagnostic and therapeutic agents. Mol Ther Nucleic Acids. 2014;3:e201. + https://github.com/obi-ontology/obi/issues/1308 + ImmPort + SOMAscan assay - + - - - population based design - A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment. - Chris Stoeckert - https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design - #1090 - population based design + + + Olink assay + + A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR. + Bjoern Peters + Hector Guzman-Orozco + Randi Vita + https://www.olink.com/ + https://github.com/obi-ontology/obi/issues/1308 + ImmPort + Olink assay - + - - + + - + - - - - - - - - - - - - - - - - - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/1 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluorescence imaging-based apoptosis assay + proximity extension assay + + An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex. + Bjoern Peters + Hector Guzman-Orozco + Randi Vita + Bjoern Peters + https://github.com/obi-ontology/obi/issues/1308 + ImmPort + proximity extension assay - + - - + + - - - - - - - - - + + + Illumina MiniSeq + Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526 + + A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + PERSON: Bonita Lam + MiniSeq + url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html + Illumina MiniSeq + + + + + + + + - + - - - - - - - - - + + + + - A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - fluroescence imaging-based cell count assay - url:http://lincsportal.ccs.miami.edu/beta/assays/31 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluorescence imaging-based cell proliferation assay + antigen detection by cytometric bead array assay + + A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest. + CMI-PB + CMI-PB + https://github.com/obi-ontology/obi/issues/1399 + antigen detection by cytometric bead array assay - + - - + + - + - - - - - - + + + + - - - - - - - + antibody detection by cytometric bead array assay + + A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. + CMI-PB + CMI-PB + https://github.com/obi-ontology/obi/issues/1399 + antibody detection by cytometric bead array assay + + + + + + + + + + + + + + + + + + - - + + + + + + + + + - - - - + + + + + + 3D molecular structure determination assay + + An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. + Bjoern Peters + Hector Guzman-Orozco + IEDB + https://github.com/obi-ontology/obi/issues/1380 + 3D molecular structure determination assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/10 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluroescence imaging-based cell cycle state assay + electron-microscopy 3D molecular structure determination assay + + A 3D molecular structure determination assay that uses electron microscopy imaging. + Bjoern Peters + Hector Guzman-Orozco + IEDB + https://github.com/obi-ontology/obi/issues/1380 + electron-microscopy 3D molecular structure determination assay - + - - + + - - + + + antigen:antibody complex + + A complex of molecular entitites which is the result of an antibody binding to an antigen. + Bjoern Peters + Hector Guzman-Orozco + IEDB + antigen:antibody complex + + + + + + + + - + - - - - - + + - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/27 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluorescence imaging-based cell viability assay + epitope:MHC:TCR complex + + A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope complex. + Bjorne Peters + Hector Guzman-Orozco + IEDB + epitope:MHC:TCR complex - + - - + + - - - - - - - - + - - - - + MHC:ligand complex + + A complex of molecular entities which is the result of a MHC molecule binding with a ligand. + Bjorne Peters + Hector Guzman-Orozco + IEDB + MHC:ligand complex + + + + + + + + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/7 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluorescence imaging-based drug synergy assay + + + + + + + + + + + + + + + + + 3D cell structure determination assay + + A 3D structure determination assay that determines the 3-dimensional configuration of a cell. + Hector Guzman-Orozco + Patrick Ray + Hector Guzman-Orozco + Patrick Ray + https://github.com/obi-ontology/obi/issues/1364 + 3D cell structure determination assay - + - - + + + + + + + + + + + + + + + + + + + + + + 3D neural cell structure determination assay + + A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell. + Hector Guzman-Orozco + Patrick Ray + Hector Guzman-Orozco + Patrick Ray + https://github.com/obi-ontology/obi/issues/1364 + Allen Institute for Brain Science + 3D neural cell structure determination assay + + + + + + + + - - - - - - - - - + + - + - - - - - - - - - + + + + - A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluorescence imaging-based cell morphology assay + neuron morphology assay + + A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron. + Hector Guzman-Orozco + Patrick Ray + Patrick Ray + https://github.com/obi-ontology/obi/issues/1364 + Allen Institute for Brain Science + neuron morphology assay - + - - + + - - - - - - - - - + + - + - - - + + + + + + + + mosaicism with repeat frameshift genetic sparse labeling + + A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons. + Patrick Ray + MORF genetic sparse labeling + https://biccn.org/teams/u01-yang + https://doi.org/10.1016/j.neuron.2020.07.019 + https://github.com/obi-ontology/obi/issues/1364 + Allen Institute for Brain Science + mosaicism with repeat frameshift genetic sparse labeling + + + + + + + + + neuron morphology reconstruction assay + + A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST). + The representation of the morphology (3D structure) of a neuron can be a summary of various measurements relating to the dimensions of the neuron in question. + Hector Guzman-Orozco + Patrick Ray + http://doi.org/10.1101/675280 + https://github.com/obi-ontology/obi/issues/1364 + Allen Institute for Brain Science + neuron morphology reconstruction assay + + + + + + + + + + + + + + - - + + + + + + + + + + + + + - - - - - - A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/8 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluorescence imaging multiplex cytological profiling + + + + + + B cell epitope assay + + An immune epitope assay that characterizes the structrue of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. + IEDB + IEDB + B cell assay|any method + B cell epitope assay - + - - - A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - protein state assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + T cell epitope assay + + An immune epitope assay that characterizes the structrue of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. + IEDB + IEDB + T cell assay|any method + T cell epitope assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:http://lincsportal.ccs.miami.edu/beta/assays/15 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluorescence imaging-based protein phosphorylation state assay + + + chemical mutagenesis + 129/Sv male mice were injected with ENU and mated to C57BL/6 females. Their first-generation (G1) male progeny were again crossed to C57BL/6 females, and then backcrossed to one of their second-generation (G2) daughters to yield a third-generation (G3). PMID:18802465 + + A form of random mutagenesis that produces a mutation by introducing the organism to a chemical mutagen. + Equivalent to FlyBase "chemical" (FBcv:0000525) in the origin of mutation branch and Dd mutagenesis meth0d term chemical mutagenesis (DDMUMET:0000014). + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/25646611/ + chemical mutagenesis - + - - - - - - - - - - - - - - - - A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - mass spectrometry-based protein state assay + + + irradiation mutagenesis + Groups of (101 x C3H)F1 hybrid male mice 11 weeks old were exposed to two different doses of 137Cs gamma rays. PMID:7035547 + + A form of random mutagenesis that produces a random mutation by exposing the organism to radiation. + Equivalent to FlyBase "irradiation" (FBcv:0000503) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + radiation induced mutagenesis + url:http://purl.obolibrary.org/obo/FBcv_0000503 + irradiation mutagenesis - + - - - A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - P100 phosphoprotein quantification assay - PMID:26912667 - PMID:29655704 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay + + + directed mutagenesis + Exons 20 and 21 were targeted for deletion because they encode the signature and Walker B motifs of the first ATP-binding domain, elements that are known to be critical for ABCA1 function. PMID:15550377 + + An induced mutation in which a specific gene(s) or part of a gene(s) is altered. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://www.ncbi.nlm.nih.gov/books/NBK21878/def-item/A4754/ + directed mutagenesis - + - - - A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - RPLA assay - RPPA assay - reverse phase lysate array profiling assay - PMID: 17041095 - PMID:31820393 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - reverse phase protein array profiling assay + + + endonuclease mediated mutagenesis + We have generated a WMS mouse model with S236X mutation in ADAMTS10 which is similar to the R237X mutation identifiedin WMS patients using CRISPR-Cas9. PMID:30060141 + + A directed mutagenesis in which guide RNAs and an endonuclease (cas9, TALEN) are used to introduce a mutation at a specific location in a gene. + Equivalent to FlyBase term "site specific cleavage" (FBcv:0003007) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/28177771/ + endonuclease mediated mutagenesis - + - - - - - - - - - - - - - - - - A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - sequential window acquisition of all theoretical mass spectra protein profiling assay - PMID:30104418 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - SWATH-MS protein profiling assay + + + cas mediated mutagenesis + Briefly, to create Adar1 M249A/M249A mice, guide RNA targeting 5’-ACCTTCTGAGCCTCTTGACA-3’ was synthesized by using Gene Art Precisiong RNA Synthesis Kit (ThermoFisherScientific). Pronuclear-stage mouse embryos (CLEA Japan Inc., Tokyo, Japan) were electroporated to introduce Cas9 mRNA, the guide RNA and a single-stranded donor... PMID:33983932 + + An endonuclease mediated mutagenesis in which guide RNAs and cas are used to introduce a mutation at a specific location in the genome. + Equivalent (narrow match) to FlyBase term "CRISPR/Cas9" (FBcv:0003008, narrow match as the OBI term covers all forms of cas) in the origin of mutation branch and Dd mutagenesis method term "CRISPR/Cas9" (DDMUMET:0000025). + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + CRISPR mediated mutagenesis + CRISPR/cas mediated mutagenesis + url:https://pubmed.ncbi.nlm.nih.gov/28177771/ + cas mediated mutagenesis - + - - - A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:12713048 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - tandem mass tag mass spectrometry assay + + + TALEN mediated mutagenesis + We designed transcription activator-like effector nucleases (TALENs) and a single-stranded oligo (ssOligo) donor template to edit the endogenous Actb locus within the mouse genome. PMID:30012594 + + An endonuclease mediated mutagenesis in which guide RNAs and transcription activator-like effector nucleases (TALENs) are used to introduce a mutation at a specific location in the genome. + Equivalent to FlyBase term "TALEN" (FBcv:0003009) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/23664777/ + TALEN mediated mutagenesis - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - fluorescence imaging-based reporter gene assay + + + zinc finger mediated mutagenesis + ZFN constructs targeting the third exon of the mouse Apoc2 gene were designed and synthetized by Sigma Aldrich... PMID:26574515 + + An endonuclease mediated mutagenesis in which synthetic zinc-finger proteins designed to target specific DNA sequences are used to introduce a mutation at a specific location in the genome. + Equivalent to FlyBase term "ZFN" (FBcv:0003239) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + ZFN mediated mutagenesis + url:https://pubmed.ncbi.nlm.nih.gov/23664777/ + zinc finger mediated mutagenesis - + - - - - - - - - - - - - - - - - - - - - - - A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - GCP - global chromatin epigenetic profiling - global chromatin profiling - PMID:25448295 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - global chromatin profiling by mass spectrometry assay + + + transgenic mutagenesis + Transgenic mice were then generated by pronuclear injection of either the mixed MoPrP-PS1 and MoPrP-APP or the bicistronic MoPrP–APP/IRES/PS1 expression cassettes into single cell embryos derived from F2 hybrids of C57BL/6J and C3H/HeJ mice... PMID:11337275 + + A form of random mutagenesis that produces a mutation by introducing a construct into the genome of an organism in a random or semi-random fashion. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/23996268/ + transgenic mutagenesis - + - - - A type of assay that identifies compounds that inhibit the activity of kinases. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CFDE - Michelle Giglio - Suvarna Nadendla - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - kinase inhibitor assay + + + gene-trap mutagenesis + Constructs lacking a promoter and including a B3-galactosidase gene, or a reporter gene encoding a protein with both B3-galactosidase and neomycin phosphotransferase activity, were designed so that activation of the reporter gene depends on its insertion within an active transcription unit. PMID:1653172 + + A transgenic mutagenesis that produces a mutation by introducing a construct designed to capture the expression of an endogenous gene by creating a spliced fusion transcript when inserted into the genome of an organism. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/17877761/ + gene-trap mutagenesis - + - - - A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://www.discoverx.com/technologies-platforms/competitive-binding-technology/kinomescan-technology-platform - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - KINOMEscan assay + + + enhancer-trap mutagenesis + We generated several lines of enhancer trap mice carrying an enhancer detector cassette expressing Cre recombinase under the transcriptional control of the minimal promoter (129 base pairs) of the mouse Thy-1.2 gene. PMID:22492032 + + A transgenic mutagenesis that produces a mutation by introducing a construct designed to monitor transcriptionally active regions when inserted into the genome of an organism by inserting a reporter gene that requires cis-acting DNA sequences in the genome to activate reporter gene expression. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/17877761/ + enhancer-trap mutagenesis - + - - - A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://www.kinativ.com/technology.html - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - KiNativ assay + + + targeted mutagenesis + To disrupt the mdr1a gene a 1.6 kb NheI genomic fragment containing exons 6 and 7 was replaced by a hygromycin phosphotransferase cassette in a targeting vector. PMID:7910522 + + A directed mutation in which a construct is used to introduce a mutation into a specific genome location through homologous recombination. + Equivalent to FlyBase term "gene targeting by homologous recombination" (FBcv:0000710) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + gene targeting by homologous recombination + url:https://pubmed.ncbi.nlm.nih.gov/23996268/ + targeted mutagenesis - + - - - A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - L1000 mRNA profiling assay - PMID:29195078 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - landmark transcript profiling assay + + + transposon-induced mutagenesis + In order to achieve SB transposon-mediated mutagenesis in mice, we employed the gene trap scheme using a novel transposon vector, and we have generated a large number of mutant mice, approximately 30% of which displayed the phenotype. PMID:16880528 + + A random mutagenesis in which expression of a transposase causes the mobilization of an artificial or modified transposable element with the insertion of the element into the genome creating a mutation. + Equivalent to FlyBase "transposable element activity" (FBcv:0000483) in the origin of mutation branch. + Susan Bello ORCID:orcid.org/0000-0003-4606-0597 + url:https://pubmed.ncbi.nlm.nih.gov/32050713/ + transposon-induced mutagenesis - + - - - A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - MEMA assay - PMID:29199020 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - microenvironment microarray assay + + + + + + + + + categorical binding datum + + A binding datum that is expressed as a categorical value. + IEDB + qualitative binding datum + IEDB + categorical binding datum - + - - - A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:28092050 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - microwestern meso-scale quantitative western blot assay + + + quantitative binding datum + + A binding datum that is expressed using numbers. + IEDB + IEDB + quantitative binding datum - + - - - - - - + + + + + - - + + + + + - - - - A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - positive/negative ion switching metabolomic assay - PMID:22498707 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - positive/negative ion switching metabolite profiling assay - - - - - - - - - A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:27925668 - PMID:29993362 - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - cyclic immunoflouroescence assay + + + + EC50 binding datum + + A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). + Bjoern Peters + Hector Guzman-Orozco + IEDB + EC50 binding datum - + - - - A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://www.bio-rad.com/en-us/applications-technologies/multiplex-immunoassays?ID=LUSM0E8UU - https://github.com/obi-ontology/obi/issues/1243 - CFDE-LINCS - multiplex bead-based protein state immunoassay + + + + + + + + + + + + + + + + + + IC50 binding datum + + A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). + Bjoern Peters + Hector Guzman-Orozco + IEDB + IC50 binding datum - + - - + + - + - - + + - - + + + + + + + - - A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. - John Judkins ORCID:0000-0001-6595-0902 - https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 - endotracheal tube specimen + + assay measuring quantitative binding of a MHC:ligand complex + + An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output. + IEDB + IEDB + quantitative binding|binding assay + assay measuring quantitative binding of a MHC:ligand complex - + - - + + - + - - + + - - + + + + + + + - - A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. - John Judkins ORCID:0000-0001-6595-0902 - https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 - endotracheal aspirate specimen + + assay measuring quantitative binding of an antigen:antibody complex + + An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output. + IEDB + IEDB + quantitative binding|binding assay + assay measuring quantitative binding of an antigen:antibody complex - + - - - When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being analyzed is the input protein sequence start site. - The position of the first amino acid in a protein sequence being analyzed (input protein sequence). - Emma Griffiths - input protein start - query protein start site - Emma Griffiths - input protein sequence start site + + + + + + + + + + + + + + + + + + + + + + assay measuring quantitative binding of an epitope:MHC:TCR complex + + An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output. + IEDB + IEDB + quantitative binding|binding assay + assay measuring quantitative binding of an epitope:MHC:TCR complex - + - - - When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence being analyzed is the input protein sequence stop site. - The position of the last amino acid in a protein sequence being analyzed (input protein sequence). - Emma Griffiths - input protein stop - query protein stop site - Emma Griffiths - input protein sequence stop site + + + albumin concentration assay + + An albumin assay that measures the concentration of albumin in a specimen. + James A. Overton + albumin concentration assay - + - - - When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence being analyzed is the input gene sequence start site. - The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). - Emma Griffiths - input gene start - query gene start site - Emma Griffiths - input gene sequence start site + + + basophil percentage assay + + A basophil assay that measures the percentage of basophils in a specimen. + James A. Overton + basophil percentage assay - + - - - When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence being analyzed is the input gene sequence stop site. - The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). - Emma Griffiths - input gene stop - query gene stop site - Emma Griffiths - input gene sequence stop site + + + calcium cation concentration assay + + A calcium cation assay that measures the concentration of calcium cations in a specimen. + James A. Overton + calcium cation concentration assay - + - - - When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being used for comparison is the reference protein sequence start site. - The position of the first amino acid in a reference protein sequence (sequence being used for comparison). - Emma Griffiths - reference protein start - subject protein start site - Emma Griffiths - reference protein sequence start site + + + chloride concentration assay + + A chloride assay that measures the concentration of chloride in a specimen. + James A. Overton + chloride concentration assay - + - - - When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence used for comparison is the reference protein sequence stop site. - The position of the last amino acid in a reference protein sequence (sequence being used for comparison). - Emma Griffiths - reference protein stop - subject protein stop site - Emma Griffiths - reference protein sequence stop site + + + cholesterol concentration assay + + A cholesterol assay that measures the concentration of cholesterol in a specimen. + James A. Overton + cholesterol concentration assay - + - - - When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence used for comparison is the reference gene sequence start site. - The position of the first nucleotide in a reference gene sequence (sequence being used for comparison). - Emma Griffiths - reference gene start - subject gene start site - Emma Griffiths - reference gene sequence start site + + + creatinine concentration assay + + A creatinine assay that measures the concentration of creatinine in a specimen. + James A. Overton + creatinine concentration assay - + - - - When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence used for comparison is the reference gene sequence stop site. - The position of the last nucelotide in a reference sequence (sequence being used for comparison). - Emma Griffiths - reference gene stop - subject gene stop site - Emma Griffiths - reference gene sequence stop site + + + eosinophil percentage assay + + An eosinophil assay that measures the percentage of eosinophils in a specimen. + James A. Overton + eosinophil percentage assay - + - - - altitude measurement datum - A length measurement datum between a point at sea or ground level and some point above it. - Chris Stoeckert - Adapted from https://www.merriam-webster.com/dictionary/altitude - altitude measurement datum + + + globulin concentration assay + + A globulin assay that measures the concentration of globulin in a specimen. + James A. Overton + globulin concentration assay - + - - - PMID:29979818 Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. - A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. - Bonita Lam - cHi-C - PMID:29979818 - https://github.com/obi-ontology/obi/issues/1251 - capture Hi-C assay + + + hemoglobin concentration assay + + A hemoglobin assay that measures the amount of hemoglobin in a specimen. + James A. Overton + hemoglobin concentration assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. - Rebecca Jackson - MRI - url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging - https://github.com/obi-ontology/obi/issues/1290 - magnetic resonance imaging assay + + + + + + + + high-density lipoprotein cholesterol concentration assay + + A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen. + James A. Overton + high-density lipoprotein cholesterol concentration assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity. - Rebecca Jackson - CAT scan - CT scan - computed tomography scan - url:https://www.mayoclinic.org/tests-procedures/ct-scan/about/pac-20393675 - https://github.com/obi-ontology/obi/issues/1290 - computed tomography imaging assay + + + iron concentration assay + + An iron assay that measures the concentration of iron cation in a specimen. + James A. Overton + iron concentration assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. - Rebecca Jackson - PET scan - positron emission tomography scan - url:https://en.wikipedia.org/wiki/Positron_emission_tomography - https://github.com/obi-ontology/obi/issues/1290 - positron emission tomography imaging assay + + + low-density lipoprotein cholesterol concentration assay + + A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen. + James A. Overton + low-density lipoprotein cholesterol concentration assay - + - - - duration of specimen collection - Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration. - A time measurement datum that is the count of collection cycles over which a specimen collection process occurs. - specimen collection duration - VEuPathDB - specimen collection duration + + + lymphocyte percentage assay + + A lymphocyte assay that measures the percentage of lymphocytes in a specimen. + James A. Overton + lymphocyte percentage assay - + - - - - - - - - - - - - - - - - - - - material supplier - A person or organization that provides material supplies to other people or organizations. - Rebecca Jackson - https://github.com/obi-ontology/obi/issues/1289 - material supplier + + + metamyelocyte count assay + + A metamyelocyte assay that measures the number of metamyelocytes in a specimen. + James A. Overton + metamyelocyte count assay - + - - - A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. - Rebecca Jackson - TCR repertoire sequencing assay - doi:10.1186/s12896-017-0379-9 - https://github.com/obi-ontology/obi/issues/1307 - T cell receptor repertoire sequencing assay + + + metamyelocyte percentage assay + + A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen. + James A. Overton + metamyelocyte percentage assay - + - - - A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. - Rebecca Jackson - Antibody repertoire sequencing assay - BCR repertoire sequencing assay - doi:10.1186/s12896-017-0379-9 - https://github.com/obi-ontology/obi/issues/1307 - B cell receptor repertoire sequencing assay + + + methemoglobin percentage assay + + A methemoglobin assay that measures the percentage of methemoglobin in a specimen. + James A. Overton + methemoglobin percentage assay - + - - - prevalence of pathogen in specimens - prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR - A data item that is the frequency of detection of a specified pathogenic organism in collected specimens. - Chris Stoeckert - prevalence of pathogen - VEuPathDB - prevalence of pathogen in specimens + + + monocyte percentage assay + + A monocyte assay that measures the percentage of monocytes in a specimen. + James A. Overton + monocyte percentage assay - + - - - prevalence of blood meal specimens from a host organism - prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal. - A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens. - Chris Stoeckert - host blood index - VEuPathDB - prevalence of blood meal specimens from a host organism + + + myelocyte count assay + + A myelocyte assay that measures the number of myelocytes in a specimen. + James A. Overton + myelocyte count assay - + - - - presence of blood from host organism in blood meal specimen - presence of blood meal host organism indicated by boolean values of yes or no. - A data item that indicates whether blood in a blood meal specimen came from a specified host organism. - Chris Stoeckert - presence of blood meal host organism - VEuPathDB - presence of blood from host organism in blood meal specimen + + + neutrophil percentage assay + + A neutrophil assay that measures the percentage of neutrophils in a specimen. + James A. Overton + neutrophil percentage assay - + - - - - - - - - - - - - - blood meal source organism - An organism that is the source of a blood meal. - Chris Stoeckert - blood meal host organism - VEuPathDB - blood meal source organism + + + phosphate ion concentration assay + + A phosphate ion assay that measures the concentration of phosphate ions in a specimen. + James A. Overton + phosphate ion concentration assay - + - - - blood meal source role - A mosquito feeds on a human whereby the human acquires the blood meal source role for the mosquito blood meal. - A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism. - Will deprecate this term in VEuPathDB ontology once in OBI. - Chris Stoeckert - http://purl.obolibrary.org/obo/EUPATH_0000791 - blood meal source role + + + potassium(1+) concentration assay + + A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen. + James A. Overton + potassium(1+) concentration assay - + - - - A role of a material entity realized in drawing an arthropod in the direction of the material. - John Judkins - attractant - IRO:0000034 - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - arthropod attractor role + + + reticulocyte percentage assay + + A reticulocyte assay that measures the percentage of reticulocytes in a specimen. + James A. Overton + reticulocyte percentage assay - + - - - An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - arthropod collection process with automated identification + + + sodium(1+) concentration assay + + A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen. + James A. Overton + sodium(1+) concentration assay - + - - - An arthropod specimen collection process that has the objective of collecting gravid female arthropods. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - gravid female arthropod specimen collection process + + + thyroid stimulating hormone concentration assay + + A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen. + James A. Overton + thyroid stimulating hormone concentration assay - + - - - An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity. - John Judkins - VSMO:0000514 - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - resting flight-capable arthropod specimen collection process + + + triglyceride concentration assay + + A triglyceride assay that measures the concentration of triglycerides in a specimen. + James A. Overton + triglyceride concentration assay - + - - - An arthropod specimen collection by aspiration that occurs in the daytime. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - daytime arthropod specimen collection by aspiration + + + 3,3',5'-triiodothyronine concentration assay + + A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen. + James A. Overton + 3,3',5'-triiodothyronine concentration assay - + - - - An arthropod specimen collection by aspiration that catches specimens resting inside a human house. - John Judkins - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - arthropod resting in human house specimen collection by aspiration + + + fibrinogen concentration assay + + A fibrinogen assay that measures the concentration of fibrinogen in a specimen. + James A. Overton + fibrinogen concentration assay - + - - - An arthropod specimen collection process that occurs while the arthropods land on a surface. - John Judkins - collection of landing insects - VSMO:0001457 - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - landing arthropod specimen collection process + + + free thyroxine concentration assay + + A thyroxine assay that measures the concentration of free thyroxine in a specimen. + James A. Overton + free thyroxine concentration assay - + - - - An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. - John Judkins - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - flying adult arthropod collection process by passive interception + + + total thyroxine concentration assay + + A thyroxine assay that measures the concentration of total thyroxine in a specimen. + James A. Overton + total thyroxine concentration assay - + - - - A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. - John Judkins - VSMO:0001355 - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - device for collection of resting adult arthropods + + + direct bilirubin concentration assay + + A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen. + James A. Overton + direct bilirubin concentration assay - + - - - A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. - John Judkins - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - well net for arthropod immatures + + + indirect bilirubin concentration assay + + A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen. + James A. Overton + indirect bilirubin concentration assay - + - - - An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller. - John Judkins - trap containing small non-human animal bait - VSMO:0001595 - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - arthropod trap containing small non-human animal bait + + + total bilirubin concentration assay + + A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen. + James A. Overton + total bilirubin concentration assay - + - - - An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage. - John Judkins - American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389 - VSMO:0001352 - https://github.com/obi-ontology/obi/issues/1302 - VEuPathDB - trap for emerging adult arthropods + + + mean cell hemoglobin assay + + A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes. + James A. Overton + mean cell hemoglobin assay - + - - - - - - - - - - - - - - - - - - An assay that measures ferritin - James A. Overton, ORCID:0000-0001-5139-5557 - OBI - ferritin assay + + + mean cell hemoglobin concentration assay + + A hemoglobin assay that measures the concentration of hemoglobin in a specimen. + James A. Overton + mean cell hemoglobin concentration assay - + - - + + + mean platelet volume assay + + A platelet assay that measures the average volume of platelets in a specimen. + James A. Overton + mean platelet volume assay + + + + + + + + + - - + - - - - + + + + + + + + + + + + + - - An assay that measures fibrinogen - James A. Overton, ORCID:0000-0001-5139-5558 - OBI - fibrinogen assay + + + + + + + + + + + + + immature neutrophil count assay + + A neutrophil assay that measures the number of immature neutrophils in a specimen. + James A. Overton + immature neutrophil count assay - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - An analyte assay that measures the abundance of iron - James A. Overton, ORCID:0000-0001-5139-5559 - OBI - iron assay + + + + + + + + + + + + + immature neutrophil percentage assay + + An neutrophil assay that measures the percentage of immature neutrophils in a specimen. + James A. Overton + immature neutrophil percentage assay - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - An analyte assay that measures the abundance of ionized calcium - James A. Overton, ORCID:0000-0001-5139-5561 - OBI - ionized calcium assay + + + + + + + + + + + + + nucleated erythrocyte percentage assay + + An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen. + James A. Overton + nucleated erythrocyte percentage assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An analyte assay that measures the abundance of transferrin - James A. Overton, ORCID:0000-0001-5139-5562 - OBI - transferrin assay + + + mean cell volume assay + + An erythrocyte assay that measures the average volume of erythrocytes in a specimen. + James A. Overton + mean cell volume assay - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - An analyte assay that measures the abundance of uric acid - James A. Overton, ORCID:0000-0001-5139-5563 - OBI - uric acid assay + + + + + + + + + + + + + erythrocyte assay + + A cytometry assay that measures the abundance and/or characteristics of erythrocytes. + James A. Overton + erythrocyte assay - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - An analyte assay that measures the abundance of globulin - James A. Overton, ORCID:0000-0001-5139-5564 - OBI - globulin assay + + + + + + + + + + + + + manual hematocrit assay + + A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes. + James A. Overton + manual hematocrit assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of myelocytes - James A. Overton, ORCID:0000-0001-5139-5565 - OBI - myelocyte assay + + adiponectin assay + + An analyte assay that measures the abundance of adiponectin + James A. Overton + adiponectin assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of metamyelocytes - James A. Overton, ORCID:0000-0001-5139-5566 - OBI - metamyelocyte assay + + adiponectin concentration assay + + An adiponectin assay that measures the concentration of adiponectin in a specimen. + James A. Overton + adiponectin concentration assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the proportion of red blood cells - James A. Overton, ORCID:0000-0001-5139-5567 - OBI - hematocrit assay + + creatine assay + + An analyte assay that measures the abundance of creatine + James A. Overton + creatine assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of promyelocytes - James A. Overton, ORCID:0000-0001-5139-5568 - OBI - promyelocyte assay + + creatine concentration assay + + A creatine assay that measures the concentration of creatine in a specimen. + James A. Overton + creatine concentration assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of basophils - James A. Overton, ORCID:0000-0001-5139-5569 - OBI - basophil assay + + estradiol assay + + An analyte assay that measures the abundance of estradiol + James A. Overton + estradiol assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of neutrophils - James A. Overton, ORCID:0000-0001-5139-5570 - OBI - neutrophil assay + + estradiol concentration assay + + An estradiol assay that measures the concentration of estradiol in a specimen. + James A. Overton + estradiol concentration assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of eosinophils - James A. Overton, ORCID:0000-0001-5139-5571 - OBI - eosinophil assay + + leptin assay + + An analyte assay that measures the abundance of leptin + James A. Overton + leptin assay - + - - + + + leptin concentration assay + + An leptin assay that measures the concentration of leptin in a specimen. + James A. Overton + leptin concentration assay + + + + + + + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of lymphocytes - James A. Overton, ORCID:0000-0001-5139-5572 - OBI - lymphocyte assay + + lipoprotein concentration assay + + An analyte assay that measures the abundance of lipoprotein + James A. Overton + lipoprotein concentration assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of monocytes - James A. Overton, ORCID:0000-0001-5139-5573 - OBI - monocyte assay + + high-density lipoprotein concentration assay + + A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen. + James A. Overton + high-density lipoprotein concentration assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of reticulocytes - James A. Overton, ORCID:0000-0001-5139-5574 - OBI - reticulocyte assay + + low-density lipoprotein concentration assay + + A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen. + James A. Overton + low-density lipoprotein concentration assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of macrophages - James A. Overton, ORCID:0000-0001-5139-5577 - OBI - macrophage assay + + very-low-density lipoprotein concentration assay + + A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen. + James A. Overton + very-low-density lipoprotein concentration assay - + - - + + + - - + - - - - + + + + + + + + + + + + + - - A cytometry assay that measures the abundance and/or characteristics of platelets - James A. Overton, ORCID:0000-0001-5139-5578 - OBI - platelet assay + + luteinizing hormone assay + + An analyte assay that measures the abundance of luteinizing hormone + James A. Overton + luteinizing hormone assay - + - - - - - - - - - barcode target locus role - An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. - Chris Stoeckert https://orcid.org/0000-0002-5714-991X - VEuPathDB - https://github.com/obi-ontology/obi/issues/1325 - barcode target locus role + + + luteinizing hormone concentration assay + + A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen. + James A. Overton + luteinizing hormone concentration assay - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + - oligonucleotide primer set - A processed material that consists of oligonucleotides that bear a primer role. - Chris Stoeckert https://orcid.org/0000-0002-5714-991X - VEuPathDB - https://github.com/obi-ontology/obi/issues/1325 - oligonucleotide primer set + nitrite assay + + An analyte assay that measures the abundance of nitrite + James A. Overton + nitrite assay - + - - - A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. - John Judkins - TaqMan - MIRO:20000102 - https://github.com/obi-ontology/obi/issues/1320 - fluorogenic PCR assay + + + nitrite concentration assay + + A nitrite assay that measures the concentration of nitrite in a specimen. + James A. Overton + nitrite concentration assay - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + - genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci. - A genotyping assay that uses polymerase chain reaction. - Chris Stoeckert, ORCID:0000-0002-5714-991X - Jie Zheng, ORCID:0000-0002-2999-0103 - VEuPathDB - https://github.com/obi-ontology/obi/issues/1348 - VEuPathDB - genotyping by PCR assay - - - - - - - - - A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CUT&RUN assay - url:https://elifesciences.org/articles/21856 - https://github.com/obi-ontology/obi/issues/1192 - bonitalam - cleavage under targets and release using nuclease assay - - - - - - - - - A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CUT&Tag assay - url:https://www.nature.com/articles/s41467-019-09982-5 - https://github.com/obi-ontology/obi/issues/1192 - bonitalam - cleavage under targets and tagmentation + phospholipid assay + + An analyte assay that measures the abundance of phospholipid + James A. Overton + phospholipid assay - + - - - Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. - A physical examination of individual that has the objective to determine the severity of coma in a patient. - John Judkins - https://github.com/obi-ontology/obi/issues/1357 - John Judkins - coma severity assay + + + phospholipid concentration assay + + A phospholipid assay that measures the concentration of phospholipids in a specimen. + James A. Overton + phospholipid concentration assay - + - - + + @@ -73169,10 +90713,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -73180,21 +90724,37 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + + progesterone assay + + An analyte assay that measures the abundance of progesterone + James A. Overton + progesterone assay + + + + + + + + + progesterone concentration assay + + A progesterone assay that measures the concentration of progesterone in a specimen. + James A. Overton + progesterone concentration assay + + + + + + + + @@ -73203,10 +90763,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -73214,26 +90774,37 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - An assay that detects Plasmodium gametocytes in a specimen. - Chris Stoeckert - Jie Zheng - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - Plasmodium gametocyte detection assay + testosterone assay + + An analyte assay that measures the abundance of testosterone + James A. Overton + testosterone assay - + - - + + + testosterone concentration assay + + A testosterone assay that measures the concentration of testosterone in a specimen. + James A. Overton + testosterone concentration assay + + + + + + + + @@ -73242,10 +90813,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -73253,21 +90824,37 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + + bile salt assay + + An analyte assay that measures the abundance of bile salt + James A. Overton + bile salt assay + + + + + + + + + bile salt concentration assay + + A bile salt assay that measures the concentration of bile salt in a specimen. + James A. Overton + bile salt concentration assay + + + + + + + + @@ -73276,10 +90863,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -73287,26 +90874,37 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. - Chris Stoeckert - Jie Zheng - malaria rapid diagnosis test - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - malaria rapid diagnosis assay + fatty acid assay + + An analyte assay that measures the abundance of fatty acid + James A. Overton + fatty acid assay - + - - + + + free fatty acid concentration assay + + A fatty acid assay that measures the concentration of free fatty acids in a specimen. + James A. Overton + free fatty acid concentration assay + + + + + + + + @@ -73315,10 +90913,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -73326,21 +90924,37 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + + insulin assay + + An analyte assay that measures the abundance of insulin + James A. Overton + insulin assay + + + + + + + + + insulin concentration assay + + A insulin assay that measures the concentration of insulin in a specimen. + James A. Overton + insulin concentration assay + + + + + + + + @@ -73349,10 +90963,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -73360,25 +90974,151 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - An assay that detects parasite in a specimen. - Chris Stoeckert - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - parasite detection assay + follicle stimulating hormone assay + + An analyte assay that measures the abundance of follicle stimulating hormone + James A. Overton + follicle stimulating hormone assay - + - - + + + follicle stimulating hormone concentration assay + + A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen. + James A. Overton + follicle stimulating hormone concentration assay + + + + + + + + + total lymphocyte count assay + + A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen. + James A. Overton + total lymphocyte count assay + + + + + + + + + total lymphocyte percentage assay + + A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen. + James A. Overton + total lymphocyte percentage assay + + + + + + + + + + + + + + + + + + + + + + fluorescent immunospot assay + + A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies. + Hector Guzman-Orozco + FLUOROSPOT + https://en.wikipedia.org/wiki/ELISpot#Mechanism_of_FluoroSpot + https://github.com/obi-ontology/obi/issues/1414 + CMI-PB + fluorescent immunospot assay + + + + + + + + + + + + + + + plasma proteomics assay + + A proteomics profiling assay that detects proteins in a blood plasma specimen. + Hector Guzman-Orozco + CMI-PB + https://github.com/obi-ontology/obi/issues/1414 + CMI-PB + plasma proteomics assay + + + + + + + + + T cell activation induced marker assay + + A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers. + Hector Guzman-Orozco + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4955771/ + https://github.com/obi-ontology/obi/issues/1414 + CMI-PB + T cell activation induced marker assay + + + + + + + + + + + + + + + leukapheresis + + A blood harvesting process in which white blood cells are separated from a blood specimen. + Hector Guzman-Orozco + https://en.wikipedia.org/wiki/Leukapheresis + leukapheresis + + + + + + + + @@ -73390,7 +91130,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -73401,7 +91141,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -73413,6 +91153,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + cerebrospinal fluid assay + + An assay that has a cerebrospinal fluid specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + cerebrospinal fluid assay + + + + + + + + @@ -73421,10 +91176,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -73432,76 +91187,36 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + - An assay that detects microorganisms in a feces specimen. - John Judkins - stool test for microorganisms - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - feces microbiology assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An assay that has a blood specimen as evaulant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - blood assay + endotracheal aspirate assay + + An assay that has an endotracheal aspirate specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + endotracheal aspirate assay - + - - + + @@ -73513,7 +91228,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -73524,7 +91239,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -73536,19 +91251,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - falcivax rapid diagnostic test + induced sputum assay + + An assay that has an induced sputum specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + induced sputum assay - + - - + + @@ -73560,7 +91277,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -73571,7 +91288,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -73583,543 +91300,168 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - optimal-IT rapid diagnostic test - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An assay that has a urine specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - urine assay - - - - - - - - - - - - - - - - - - - - - - An organism identification assay that identifies the species of parasites by PCR. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - parasite species identification by PCR assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - An assay that detects parasite in a specimen using PCR. - Chris Stoeckert - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - parasite detection by PCR assay - - - - - - - - - Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658] - An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die. - VEuPathDB - VSMO:0001649 - free-standing window trap - - - - - - - - - - - - - - - A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin. - VEuPathDB - BG-lure - IRO:0001060 - BG-lure scent dispenser - - - - - - - - - A device that consists of a network of mesh and is designed to capture adult arthropods. - VEuPathDB - VSMO:0001522 - hand-held sweep net - - - - - - - - - The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658] - A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan. - VEuPathDB - CDC gravid trap - VSMO:0001510 - Centers for Disease Control and Prevention gravid trap - - - - - - - - - An arthropod specimen collection process in which the arthropods are in the embryo stage. - VEuPath - collection of eggs - MIRO:30000049 - https://github.com/obi-ontology/obi/issues/1322 - egg specimen collection process - - - - - - - - - An arthropod specimen collection process in which the arthropods are in the larval stage. - VEuPath - collection of larvae - MIRO:30000022 - https://github.com/obi-ontology/obi/issues/1322 - larval specimen collection process - - - - - - - - - An arthropod specimen collection process in which the arthropods are in the pupal stage. - VEuPath - collection of pupae - MIRO:30000050 - https://github.com/obi-ontology/obi/issues/1322 - pupal specimen collection process + lung assay + + An assay that has a lung specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + lung assay - + - + + - - - + + + + + + + + + + + + - - + + + + + + + + + + + + - A blood specimen that is located in a vacutainer. - John Judkins - Vacutainer sample - VEuPathDB - blood specimen in vacutainer + milk assay + + An assay that has a milk specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + milk assay - + - + + - - - + + + + + + + + + + + + - - + + + + + + + + + + + + - A blood specimen that is located on a filter paper. - Chris Stoeckert - Jie Zheng - Filter paper sample - Penn Group - blood specimen on filter paper - - - - - - - - - A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads. - John Judkins - VEuPathDB - proportion mapped reads - - - - - - - - - - - - - - - - - - - - - - - - - Administering substance in vivo where an antibiotic substance is administered to a living organism. - Chris Stoeckert - Cristian Cocos - Jie Zheng - Penn Group - antibiotic administration process - - - - - - - - - A data item that is about resistance to an insecticide. - John Judkins - VEuPathDB - insecticide resistance datum - - - - - - - - - A data item that is the specified output of an organism identification assay. - John Judkins - VEuPathDB - organism identification datum - - - - - - - - - A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. - Easting and northing coordinates are commonly measured in meters from a horizontal datum. - John Judkins - https://en.wikipedia.org/wiki/Grid_reference_system - easting coordinate measurement datum - - - - - - - - - A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. - Easting and northing coordinates are commonly measured in meters from a horizontal datum. - John Judkins - https://en.wikipedia.org/wiki/Grid_reference_system - northing coordinate measurement datum - - - - - - - - - Organization that undertakes a clinical study at some point in time. - Chris Stoeckert - Cristian Cocos - Jie Zheng - Penn Group - clinical study center - - - - - - - - - A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. + feces assay + + An assay that has a feces specimen as evaluant. John Judkins VEuPathDB - sequencing protocol + https://github.com/obi-ontology/obi/issues/1429 + feces assay - + - - + + - - - - - - A protocol that specifies processes to fulfill a specimen collection objective. - John Judkins - VEuPathDB - specimen collection protocol - - - - - - - - - - + - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - A symbol that denotes a participant under investigation. - John Judkins - VEuPathDB - participant identifier - - - - - - - - - A temperature measurement datum that is about an axilla. - John Judkins - VEuPathDB - axillary temperature measurement datum - - - - - - - - - A temperature measurement datum that is about an organism. - Chris Stoeckert - Jie Zheng - Penn Group - organismal body temperature measurement datum - - - - - - - - - - - - - - A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized. - John Judkins - https://en.wikipedia.org/wiki/Common_name - common name of organism - - - - - - - - - An age since birth measurement datum at the time of subject enrollment. - Jie Zheng - Penn Group - age since birth at time of enrollment - - - - - - - - - An age since birth measurement datum at the time of a clinical visit. - Chris Stoeckert - Grant Dorsey - Jie Zheng - Shon Cade - Penn Group - age since birth at time of visit - - - - - - - - - A data item that is about a collection of insects. - John Judkins - entomological measurement datum - VEuPathDB - entomological data item - - - - - - - - - A scalar measurement datum that is the result of measuring temperature. + umbilical cord blood assay + + An assay that has an umbilical cord blood specimen as evaluant. John Judkins VEuPathDB - temperature measurement datum + https://github.com/obi-ontology/obi/issues/1429 + umbilical cord blood assay - + - - + + @@ -74131,7 +91473,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -74142,7 +91484,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -74154,124 +91496,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An assay that detects body temperature of an organism. - Chris Stoeckert - Jie Zheng - VEuPathDB - https://github.com/obi-ontology/obi/issues/1322 - organismal body temperature measurement assay - - - - - - - - - extraction date - A time measurement datum that specifies when some material was extracted from an input material. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - FLU, VEuPathDB - https://github.com/obi-ontology/obi/issues/1286 - extraction date - - - - - - - - - extraction duration time - A time measurement datum that is the result of measuring the duration of an extraction process. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - Meredith Keybl, Shane Babcock - https://github.com/obi-ontology/obi/issues/1286 - extraction duration time - - - - - - - - - specimen collection time post disease onset - A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - GROUP:FLU, Shane Babcock - https://github.com/obi-ontology/obi/issues/1286 - specimen collection time post disease onset - - - - - - - - - specimen collection time post infection - A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - VEuPathDB, EUPATH:0000613 - https://github.com/obi-ontology/obi/issues/1286 - specimen collection time post infection - - - - - - - - - laboratory postal address - A postal address used as a directive to deliver something to a laboratory. - Chris Stoeckert, ORCID: 0000-0002-5714-991X - laboratory address - GROUP:FLU, Shane Babcock - https://github.com/obi-ontology/obi/issues/1286 - laboratory postal address - - - - - - - - - laboratory-based population - Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033) - A population where the collection of individuals is located and maintained in a laboratory, research, or production facility. - Chris Stoeckert, ORCID: 0000-0002-5714-991X + saliva assay + + An assay that has a saliva specimen as evaluant. + John Judkins VEuPathDB - https://github.com/obi-ontology/obi/issues/1370 - laboratory-based population - - - - - - - - - A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - intrinsic fluorescence assay - PMID:25578980 - url:https://en.wikipedia.org/wiki/Autofluorescence - https://github.com/obi-ontology/obi/issues/1393 - CFDE - autofluorescence assay + https://github.com/obi-ontology/obi/issues/1429 + saliva assay - + - - + + @@ -74280,10 +91519,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -74291,154 +91530,36 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + - An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:25578980 - url:https://en.wikipedia.org/wiki/Autofluorescence - https://github.com/obi-ontology/obi/issues/1394 - CFDE - autofluorescence microscopy assay - - - - - - - - - An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - bulk ATAC-seq - PMID:24097267 - https://github.com/obi-ontology/obi/issues/1395 - CFDE - bulk assay for transposase-accessible chromatin using sequencing - - - - - - - - - An RNA-seq assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://www.biostars.org/p/458516/ - https://github.com/obi-ontology/obi/issues/1396 - CFDE - bulk RNA-seq assay - - - - - - - - - - - - - - - - - - - - - - An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PMID:29993362 - https://github.com/obi-ontology/obi/issues/1397 - CFDE - multiplexed fluorescent antibody imaging assay - - - - - - - - - A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://cancerres.aacrjournals.org/content/80/16_Supplement/1448 - url:https://www.cytivalifesciences.co.kr/wp-content/uploads/2020/07/Cell-DIVE-Tech-Info-Sheet-CY11898-09Apr20-DF.pdf - https://github.com/obi-ontology/obi/issues/1398 - CFDE - Cell DIVE multiplexed imaging assay - - - - - - - - - A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - CODEX - url:https://www.scilifelab.se/facilities/co-detection-by-indexing-codex/ - https://github.com/obi-ontology/obi/issues/1399 - CFDE - co-detection by indexing assay - - - - - - - - - - - - - - - - - - - - - - An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - FISH - url:https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization - https://github.com/obi-ontology/obi/issues/1400 - CFDE - fluorescence in-situ hybridization assay + cerebrospinal fluid microbiology assay + + An organism identification assay that has a cerebrospinal fluid specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + cerebrospinal fluid microbiology assay - + - - + + @@ -74450,7 +91571,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -74461,7 +91582,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -74473,6 +91594,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + endotracheal tube aspirate microbiology assay + + An organism identification assay that has an endotracheal aspirate specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + endotracheal tube aspirate microbiology assay + + + + + + + + @@ -74481,10 +91617,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -74492,2020 +91628,1967 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - DARTFISH - url:http://genome-tech.ucsd.edu/ZhangLab/index.php/data/tech-dev/ - url:http://www.weizmann.ac.il/conferences/SCG2015/sites/conferences.SCG2015/files/scg_2015_abstractbook_online_version.pdf - url:https://escholarship.org/uc/item/5bq3128f - https://github.com/obi-ontology/obi/issues/1401 - CFDE - decoding amplified targeted transcripts with fluorescence in situ hybridization assay - - - - - - - - - A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - IMC - imaging CyTOF - PMID:31798587 - https://github.com/obi-ontology/obi/issues/1403 - CFDE - imaging mass cytometry assay - - - - - - - - - - - - - - + - - + + - - - - - A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - LC-MS - CHMO:0000524 - https://github.com/obi-ontology/obi/issues/1404 - CFDE - liquid chromatography mass spectrometry assay - - - - - - - - - A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/light-sheet-fluorescence-microscopy - https://github.com/obi-ontology/obi/issues/1405 - CFDE - lightsheet fluorescence microscopy assay - - - - - - - - - A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - MALDI-IMS - url:http://purl.obolibrary.org/obo/CHMO_0000054 - https://github.com/obi-ontology/obi/issues/1406 - CFDE - matrix assisted laser desorption ionization imaging mass spectrometry assay - - - - - - - - - A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - MIBI - url:https://www.nature.com/articles/s41374-020-0417-4 - https://github.com/obi-ontology/obi/issues/1407 - CFDE - multiplexed ion beam imaging assay - - - - - - - - - A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - NanoDESI - url:https://pubmed.ncbi.nlm.nih.gov/20593081/ - https://github.com/obi-ontology/obi/issues/1408 - CFDE - nanospray desorption electrospray ionization assay + induced sputum microbiology assay + + An organism identification assay that has an induced sputum specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + induced sputum microbiology assay - + - - + + - - - - - - - - - + + - A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - NanoPOTS - url:https://www.emsl.pnnl.gov/science/related-instrument/nanodroplet-processing-in-one-pot-for-trace-samples--nanopots-/1806 - https://github.com/obi-ontology/obi/issues/1409 - CFDE - nanodroplet processing in one pot for trace samples assay - - - - - - - - - A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - PAS staining - url:https://microbenotes.com/periodic-acid-schiff-pas-staining/ - https://github.com/obi-ontology/obi/issues/1410 - CFDE - periodic acid-Schiff staining assay - - - - - - - - - An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - sciATACseq - url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158300/ - https://github.com/obi-ontology/obi/issues/1411 - CFDE - single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing - - - - - - - - - A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - sciRNAseq - url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894354/ - https://github.com/obi-ontology/obi/issues/1412 - CFDE - single-cell combinatorial indexing RNA sequencing assay + blood assay datum + + A data item that is the specified output of a blood assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + blood assay datum - + - - - A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - seqFISH - url:https://spatial.caltech.edu/seqfish/ - https://github.com/obi-ontology/obi/issues/1413 - CFDE - sequential fluorescence in-situ hybridization assay + + + + + + + + + blood microbiology datum + + An organism identification datum that is the specified output of a blood microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + blood microbiology datum - + - - - An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - url:https://science.sciencemag.org/content/363/6434/1463 - https://github.com/obi-ontology/obi/issues/1414 - CFDE - slide-seq assay + + + + + + + + + feces assay datum + + A data item that is the specified output of a feces assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + feces assay datum - + - - - A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - SNARE-seq - SNAREseq - url:https://www.nature.com/articles/s41587-019-0290-0 - https://github.com/obi-ontology/obi/issues/1416 - CFDE - single-nucleus chromatin accessibility and mRNA expression sequencing assay + + + + + + + + + feces microbiology datum + + An organism identification datum that is the specified output of a feces microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + feces microbiology datum - + - - - A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - sNuc-seq - single nuclei RNA sequencing - snRNA-seq - EFO:0009809 - url:https://www.biocompare.com/Editorial-Articles/557506-Advantages-of-Single-Nucleus-RNA-Sequencing/ - https://github.com/obi-ontology/obi/issues/1415 - CFDE - single-nucleus RNA sequencing assay + + + + + + + + + urine assay datum + + A data item that is the specified output of a urine assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + urine assay datum - + - - - A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds. - Michelle Giglio - Rebecca Jackson - Suvarna Nadendla - GC-MS - url:http://purl.bioontology.org/ontology/MESH/D008401 - https://github.com/obi-ontology/obi/issues/1417 - CFDE - gas chromatography mass spectrometry assay + + + + + + + + + urine microbiology datum + + An organism identification datum that is the specified output of a urine microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + urine microbiology datum - + - - - An analyte assay that uses aptamers to detect protein analytes in serum. - Bjoern Peters - Randi Vita - Rohloff JC, et al. Nucleic acid ligands with protein-like side chains: modified aptamers and their uses as diagnostic and therapeutic agents. Mol Ther Nucleic Acids. 2014;3:e201. - https://github.com/obi-ontology/obi/issues/1308 - ImmPort - SOMAscan assay + + + + + + + + + induced sputum assay datum + + A data item that is the specified output of a induced sputum assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + induced sputum assay datum - + - - - A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR. - Bjoern Peters - Hector Guzman-Orozco - Randi Vita - https://www.olink.com/ - https://github.com/obi-ontology/obi/issues/1308 - ImmPort - Olink assay + + + + + + + + + induced sputum microbiology datum + + An organism identification datum that is the specified output of an induced sputum microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + induced sputum microbiology datum - + - - + + - - - - - - - - - + + - An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex. - Bjoern Peters - Hector Guzman-Orozco - Randi Vita - Bjoern Peters - https://github.com/obi-ontology/obi/issues/1308 - ImmPort - proximity extension assay + cerebrospinal fluid assay datum + + A data item that is the specified output of a cerebrospinal fluid assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + cerebrospinal fluid assay datum - + - - + + - - + + - Illumina MiniSeq - Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526 - A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. - PERSON: Bonita Lam - MiniSeq - url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html - Illumina MiniSeq + cerebrospinal fluid microbiology datum + + An organism identification datum that is the specified output of a cerebrospinal fluid microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + cerebrospinal fluid microbiology datum - + - - + + - - - - - - - + + - A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest. - CMI-PB - CMI-PB - https://github.com/obi-ontology/obi/issues/1399 - antigen detection by cytometric bead array assay + endotracheal aspirate assay datum + + An organism identification datum that is the specified output of an endotracheal aspirate assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + endotracheal aspirate assay datum - + - - + + - - - - - - - + + - A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. - CMI-PB - CMI-PB - https://github.com/obi-ontology/obi/issues/1399 - antibody detection by cytometric bead array assay + endotracheal tube aspirate microbiology datum + + An organism identification datum that is the specified output of an endotracheal tube aspirate microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + endotracheal tube aspirate microbiology datum - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. - Bjoern Peters - Hector Guzman-Orozco - IEDB - https://github.com/obi-ontology/obi/issues/1380 - 3D molecular structure determination assay + + + + + + + + + lung microbiology datum + + An organism identification datum that is the specified output of a lung microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + lung microbiology datum - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - A 3D molecular structure determination assay that uses electron microscopy imaging. - Bjoern Peters - Hector Guzman-Orozco - IEDB - https://github.com/obi-ontology/obi/issues/1380 - electron-microscopy 3D molecular structure determination assay + nasopharyngeal or oropharyngeal swab microbiology datum + + An organism identification datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + nasopharyngeal or oropharyngeal swab microbiology datum - + - - + + - - - - - - - - - + + - A complex of molecular entitites which is the result of an antibody binding to an antigen. - Bjoern Peters - Hector Guzman-Orozco - IEDB - antigen:antibody complex + pleural fluid microbiology datum + + An organism identification datum that is the specified output of a pleural fluid microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + pleural fluid microbiology datum - + - - + + - - - - - - - - - + + - A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope complex. - Bjorne Peters - Hector Guzman-Orozco - IEDB - epitope:MHC:TCR complex + umbilical cord blood assay datum + + An organism identification datum that is the specified output of an umbilical cord blood assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + umbilical cord blood assay datum - + - - + + - - + + - A complex of molecular entities which is the result of a MHC molecule binding with a ligand. - Bjorne Peters - Hector Guzman-Orozco - IEDB - MHC:ligand complex + umbilical cord blood microbiology datum + + An organism identification datum that is the specified output of an umbilical cord blood microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + umbilical cord blood microbiology datum - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A 3D structure determination assay that determines the 3-dimensional configuration of a cell. - Hector Guzman-Orozco - Patrick Ray - Hector Guzman-Orozco - Patrick Ray - https://github.com/obi-ontology/obi/issues/1364 - 3D cell structure determination assay + + + + + + + + + bacteria in blood datum + + A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in blood datum - + - - - - - - - - - - - - - - - - - - - - - - A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell. - Hector Guzman-Orozco - Patrick Ray - Hector Guzman-Orozco - Patrick Ray - https://github.com/obi-ontology/obi/issues/1364 - Allen Institute for Brain Science - 3D neural cell structure determination assay + + + + + + + + + virus in blood datum + + A blood microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in blood datum - + - - - - - - - - + + - - - - - - - + + - A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron. - Hector Guzman-Orozco - Patrick Ray - Patrick Ray - https://github.com/obi-ontology/obi/issues/1364 - Allen Institute for Brain Science - neuron morphology assay + eukaryota in blood datum + + A blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in blood datum - + - - - - - - - - + + - - - - - - - + + - A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons. - Patrick Ray - MORF genetic sparse labeling - https://biccn.org/teams/u01-yang - https://doi.org/10.1016/j.neuron.2020.07.019 - https://github.com/obi-ontology/obi/issues/1364 - Allen Institute for Brain Science - mosaicism with repeat frameshift genetic sparse labeling + bacteria in feces datum + + A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in feces datum - + - - - A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST). - The representation of the morphology (3D structure) of a neuron can be a summary of various measurements relating to the dimensions of the neuron in question. - Hector Guzman-Orozco - Patrick Ray - http://doi.org/10.1101/675280 - https://github.com/obi-ontology/obi/issues/1364 - Allen Institute for Brain Science - neuron morphology reconstruction assay + + + + + + + + + eukaryota in feces datum + + A feces microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in feces datum - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immune epitope assay that characterizes the structrue of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. - IEDB - IEDB - B cell assay|any method - B cell epitope assay + + + + + + + + + virus in feces datum + + A feces microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in feces datum - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immune epitope assay that characterizes the structrue of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. - IEDB - IEDB - T cell assay|any method - T cell epitope assay + + + + + + + + + eukaryota in urine datum + + A urine microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in urine datum - + - - - 129/Sv male mice were injected with ENU and mated to C57BL/6 females. Their first-generation (G1) male progeny were again crossed to C57BL/6 females, and then backcrossed to one of their second-generation (G2) daughters to yield a third-generation (G3). PMID:18802465 - A form of random mutagenesis that produces a mutation by introducing the organism to a chemical mutagen. - Equivalent to FlyBase "chemical" (FBcv:0000525) in the origin of mutation branch and Dd mutagenesis meth0d term chemical mutagenesis (DDMUMET:0000014). - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - url:https://pubmed.ncbi.nlm.nih.gov/25646611/ - chemical mutagenesis + + + + + + + + + bacteria in induced sputum datum + + An induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in induced sputum datum - + - - - Groups of (101 x C3H)F1 hybrid male mice 11 weeks old were exposed to two different doses of 137Cs gamma rays. PMID:7035547 - A form of random mutagenesis that produces a random mutation by exposing the organism to radiation. - Equivalent to FlyBase "irradiation" (FBcv:0000503) in the origin of mutation branch. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - radiation induced mutagenesis - url:http://purl.obolibrary.org/obo/FBcv_0000503 - irradiation mutagenesis + + + + + + + + + eukaryota in induced sputum datum + + An induced sputum microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in induced sputum datum - + - - - Exons 20 and 21 were targeted for deletion because they encode the signature and Walker B motifs of the first ATP-binding domain, elements that are known to be critical for ABCA1 function. PMID:15550377 - An induced mutation in which a specific gene(s) or part of a gene(s) is altered. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - url:https://www.ncbi.nlm.nih.gov/books/NBK21878/def-item/A4754/ - directed mutagenesis + + + + + + + + + virus in induced sputum datum + + An induced sputum microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in induced sputum datum - + - - - We have generated a WMS mouse model with S236X mutation in ADAMTS10 which is similar to the R237X mutation identifiedin WMS patients using CRISPR-Cas9. PMID:30060141 - A directed mutagenesis in which guide RNAs and an endonuclease (cas9, TALEN) are used to introduce a mutation at a specific location in a gene. - Equivalent to FlyBase term "site specific cleavage" (FBcv:0003007) in the origin of mutation branch. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - url:https://pubmed.ncbi.nlm.nih.gov/28177771/ - endonuclease mediated mutagenesis + + + + + + + + + bacteria in endotracheal tube aspirate datum + + An endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in endotracheal tube aspirate datum - + - - - Briefly, to create Adar1 M249A/M249A mice, guide RNA targeting 5’-ACCTTCTGAGCCTCTTGACA-3’ was synthesized by using Gene Art Precisiong RNA Synthesis Kit (ThermoFisherScientific). Pronuclear-stage mouse embryos (CLEA Japan Inc., Tokyo, Japan) were electroporated to introduce Cas9 mRNA, the guide RNA and a single-stranded donor... PMID:33983932 - An endonuclease mediated mutagenesis in which guide RNAs and cas are used to introduce a mutation at a specific location in the genome. - Equivalent (narrow match) to FlyBase term "CRISPR/Cas9" (FBcv:0003008, narrow match as the OBI term covers all forms of cas) in the origin of mutation branch and Dd mutagenesis method term "CRISPR/Cas9" (DDMUMET:0000025). - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - CRISPR mediated mutagenesis - CRISPR/cas mediated mutagenesis - url:https://pubmed.ncbi.nlm.nih.gov/28177771/ - cas mediated mutagenesis + + + + + + + + + bacteria in lung datum + + A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in lung datum - + - - - We designed transcription activator-like effector nucleases (TALENs) and a single-stranded oligo (ssOligo) donor template to edit the endogenous Actb locus within the mouse genome. PMID:30012594 - An endonuclease mediated mutagenesis in which guide RNAs and transcription activator-like effector nucleases (TALENs) are used to introduce a mutation at a specific location in the genome. - Equivalent to FlyBase term "TALEN" (FBcv:0003009) in the origin of mutation branch. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - url:https://pubmed.ncbi.nlm.nih.gov/23664777/ - TALEN mediated mutagenesis + + + + + + + + + eukaryota in lung datum + + A lung microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in lung datum - + - - - ZFN constructs targeting the third exon of the mouse Apoc2 gene were designed and synthetized by Sigma Aldrich... PMID:26574515 - An endonuclease mediated mutagenesis in which synthetic zinc-finger proteins designed to target specific DNA sequences are used to introduce a mutation at a specific location in the genome. - Equivalent to FlyBase term "ZFN" (FBcv:0003239) in the origin of mutation branch. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - ZFN mediated mutagenesis - url:https://pubmed.ncbi.nlm.nih.gov/23664777/ - zinc finger mediated mutagenesis + + + + + + + + + virus in lung datum + + A lung microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in lung datum - + - - - Transgenic mice were then generated by pronuclear injection of either the mixed MoPrP-PS1 and MoPrP-APP or the bicistronic MoPrP–APP/IRES/PS1 expression cassettes into single cell embryos derived from F2 hybrids of C57BL/6J and C3H/HeJ mice... PMID:11337275 - A form of random mutagenesis that produces a mutation by introducing a construct into the genome of an organism in a random or semi-random fashion. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - url:https://pubmed.ncbi.nlm.nih.gov/23996268/ - transgenic mutagenesis + + + + + + + + + bacteria in nasopharyngeal or oropharyngeal swab datum + + A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in nasopharyngeal or oropharyngeal swab datum - + - - - Constructs lacking a promoter and including a B3-galactosidase gene, or a reporter gene encoding a protein with both B3-galactosidase and neomycin phosphotransferase activity, were designed so that activation of the reporter gene depends on its insertion within an active transcription unit. PMID:1653172 - A transgenic mutagenesis that produces a mutation by introducing a construct designed to capture the expression of an endogenous gene by creating a spliced fusion transcript when inserted into the genome of an organism. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - url:https://pubmed.ncbi.nlm.nih.gov/17877761/ - gene-trap mutagenesis + + + + + + + + + eukaryota in nasopharyngeal or oropharyngeal swab datum + + A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in nasopharyngeal or oropharyngeal swab datum - + - - - We generated several lines of enhancer trap mice carrying an enhancer detector cassette expressing Cre recombinase under the transcriptional control of the minimal promoter (129 base pairs) of the mouse Thy-1.2 gene. PMID:22492032 - A transgenic mutagenesis that produces a mutation by introducing a construct designed to monitor transcriptionally active regions when inserted into the genome of an organism by inserting a reporter gene that requires cis-acting DNA sequences in the genome to activate reporter gene expression. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - url:https://pubmed.ncbi.nlm.nih.gov/17877761/ - enhancer-trap mutagenesis + + + + + + + + + virus in nasopharyngeal or oropharyngeal swab datum + + A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in nasopharyngeal or oropharyngeal swab datum - + - - - To disrupt the mdr1a gene a 1.6 kb NheI genomic fragment containing exons 6 and 7 was replaced by a hygromycin phosphotransferase cassette in a targeting vector. PMID:7910522 - A directed mutation in which a construct is used to introduce a mutation into a specific genome location through homologous recombination. - Equivalent to FlyBase term "gene targeting by homologous recombination" (FBcv:0000710) in the origin of mutation branch. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - gene targeting by homologous recombination - url:https://pubmed.ncbi.nlm.nih.gov/23996268/ - targeted mutagenesis + + + + + + + + + bacteria in pleural fluid datum + + A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + bacteria in pleural fluid datum - + - - - In order to achieve SB transposon-mediated mutagenesis in mice, we employed the gene trap scheme using a novel transposon vector, and we have generated a large number of mutant mice, approximately 30% of which displayed the phenotype. PMID:16880528 - A random mutagenesis in which expression of a transposase causes the mobilization of an artificial or modified transposable element with the insertion of the element into the genome creating a mutation. - Equivalent to FlyBase "transposable element activity" (FBcv:0000483) in the origin of mutation branch. - Susan Bello ORCID:orcid.org/0000-0003-4606-0597 - url:https://pubmed.ncbi.nlm.nih.gov/32050713/ - transposon-induced mutagenesis + + + + + + + + + eukaryota in pleural fluid datum + + A pleural fluid microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in pleural fluid datum - + - - + + - - + + - A binding datum that is expressed as a categorical value. - IEDB - qualitative binding datum - IEDB - categorical binding datum + virus in pleural fluid datum + + A pleural fluid microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + virus in pleural fluid datum - + - - - A binding datum that is expressed using numbers. - IEDB - IEDB - quantitative binding datum + + + + + + + + + eukaryota in umbilical cord blood datum + + An umbilical cord blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1428 + eukaryota in umbilical cord blood datum - + - - + + + - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). - Bjoern Peters - Hector Guzman-Orozco - IEDB - EC50 binding datum + + lung microbiology assay + + An organism identification assay that has a lung specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + lung microbiology assay - + - - + + + - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). - Bjoern Peters - Hector Guzman-Orozco - IEDB - IC50 binding datum + + pleural fluid microbiology assay + + An organism identification assay that has a pleural fluid specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + pleural fluid microbiology assay - + - - + + + - - - + + + + + + + + + + + + - + - - - - + + + + + + + + + - - An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output. - IEDB - IEDB - quantitative binding|binding assay - assay measuring quantitative binding of a MHC:ligand complex + + umbilical cord blood microbiology assay + + An organism identification assay that has an umbilical cord blood specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + umbilical cord blood microbiology assay - + - - + + + - - - + + + + + + + + + + + + + + + + + + + - + - - - - + + + + + + + + + + + + + + - - An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output. - IEDB - IEDB - quantitative binding|binding assay - assay measuring quantitative binding of an antigen:antibody complex + + nasopharyngeal or oropharyngeal swab microbiology assay + + An organism identification assay that has a nasopharyngeal or oropharyngeal swab specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + nasopharyngeal or oropharyngeal swab microbiology assay - + - - + + + - - - + + + + + + + + + + + + - + - - - - + + + + + + + + + - - An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output. - IEDB - IEDB - quantitative binding|binding assay - assay measuring quantitative binding of an epitope:MHC:TCR complex - - - - - - - - - An albumin assay that measures the concentration of albumin in a specimen. - James A. Overton - albumin concentration assay - - - - - - - - - A basophil assay that measures the percentage of basophils in a specimen. - James A. Overton - basophil percentage assay - - - - - - - - - A calcium cation assay that measures the concentration of calcium cations in a specimen. - James A. Overton - calcium cation concentration assay - - - - - - - - - A chloride assay that measures the concentration of chloride in a specimen. - James A. Overton - chloride concentration assay - - - - - - - - - A cholesterol assay that measures the concentration of cholesterol in a specimen. - James A. Overton - cholesterol concentration assay - - - - - - - - - A creatinine assay that measures the concentration of creatinine in a specimen. - James A. Overton - creatinine concentration assay - - - - - - - - - An eosinophil assay that measures the percentage of eosinophils in a specimen. - James A. Overton - eosinophil percentage assay - - - - - - - - - A globulin assay that measures the concentration of globulin in a specimen. - James A. Overton - globulin concentration assay - - - - - - - - - A hemoglobin assay that measures the amount of hemoglobin in a specimen. - James A. Overton - hemoglobin concentration assay - - - - - - - - - A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen. - James A. Overton - high-density lipoprotein cholesterol concentration assay - - - - - - - - - An iron assay that measures the concentration of iron cation in a specimen. - James A. Overton - iron concentration assay + + urine microbiology assay + + An organism identification assay that has a urine specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1429 + urine microbiology assay - + - - - A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen. - James A. Overton - low-density lipoprotein cholesterol concentration assay + + + multiplex real time polymerase chain reaction assay + + A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. + John Judkins + multiplexed real time polymerase chain reaction assay + VEuPathDB + https://github.com/obi-ontology/obi/issues/1431 + multiplex real time polymerase chain reaction assay - + - - - A lymphocyte assay that measures the percentage of lymphocytes in a specimen. - James A. Overton - lymphocyte percentage assay + + + multiplex real time reverse-transcription polymerase chain reaction assay + + A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. + John Judkins + multiplexed real time reverse-transcription polymerase chain reaction assay + VEuPathDB + https://github.com/obi-ontology/obi/issues/1431 + multiplex real time reverse-transcription polymerase chain reaction assay - + - - - A metamyelocyte assay that measures the number of metamyelocytes in a specimen. - James A. Overton - metamyelocyte count assay + + + mosquito membrane feeding device + + A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1439 + mosquito membrane feeding device - + - - - A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen. - James A. Overton - metamyelocyte percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mosquito membrane feeding assay + Testing the effectiveness of drugs or antibodies against parasite transmission. + + An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1439 + mosquito membrane feeding assay - + - - - A methemoglobin assay that measures the percentage of methemoglobin in a specimen. - James A. Overton - methemoglobin percentage assay + + + in silico design + + A study design that is executed primarily on a computer. + Hector Guzman-Orozco + https://en.wikipedia.org/wiki/In_silico + https://github.com/obi-ontology/obi/issues/1430 + CMI-PB + in silico design - + - - - A monocyte assay that measures the percentage of monocytes in a specimen. - James A. Overton - monocyte percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific granulysin release by T cells + + A cytometric bead array assay that detects epitope specific granulysin release by T cells. + IEDB + IEDB + granulysin release|cytometric bead array + cytometric bead array assay measuring epitope specific granulysin release by T cells - + - - - A myelocyte assay that measures the number of myelocytes in a specimen. - James A. Overton - myelocyte count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytometric bead array assay measuring epitope specific perforin release by T cells + + A cytometric bead array assay that detects epitope specific perforin release by T cells. + IEDB + IEDB + perforin release|cytometric bead array + cytometric bead array assay measuring epitope specific perforin release by T cells - + - - - A neutrophil assay that measures the percentage of neutrophils in a specimen. - James A. Overton - neutrophil percentage assay + + + + + + + + + modified acid-fast stain microscopy assay + + A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. + John Judkins + NCIT:C85736 + https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html + https://github.com/obi-ontology/obi/issues/1444 + modified acid-fast stain microscopy assay - + - - - A phosphate ion assay that measures the concentration of phosphate ions in a specimen. - James A. Overton - phosphate ion concentration assay + + + positive binding datum + + A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. + Bjoern Peters + Hector Guzman-Orozco + IEDB + positive binding datum - + - - - A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen. - James A. Overton - potassium(1+) concentration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + antibodies from lymphocyte secretions assay + PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes. + + An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. + John Judkins + ALS assay + antibodies from lymphocyte supernatant assay + OBI + VEuPathDB + https://github.com/obi-ontology/obi/issues/1443 + antibodies from lymphocyte secretions assay - + - - - A reticulocyte assay that measures the percentage of reticulocytes in a specimen. - James A. Overton - reticulocyte percentage assay + + + tyramide signal amplification sequencing assay + + A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm. + Michelle Giglio + Suvarna Nadendla + TSA-seq + EFO:0009971 + PMID:30154186 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + tyramide signal amplification sequencing assay - + - - - A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen. - James A. Overton - sodium(1+) concentration assay + + + DNA adenine methyltransferase identification assay + + An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed. + Michelle Giglio + Suvarna Nadendla + DamID assay + EFO:0008704 + PMID:17545983 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + DNA adenine methyltransferase identification assay - + - - - A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen. - James A. Overton - thyroid stimulating hormone concentration assay + + + + + + + + + + + + + + + + DamID-seq + + A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site. + Michelle Giglio + Suvarna Nadendla + 4DN DCIC + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + DamID-seq - + - - - A triglyceride assay that measures the concentration of triglycerides in a specimen. - James A. Overton - triglyceride concentration assay + + + nucleolus-associated domain sequencing assay + + A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains. + Michelle Giglio + Suvarna Nadendla + NAD-seq + EFO:0009972 + PMID:31201210 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + nucleolus-associated domain sequencing assay - + - - - A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen. - James A. Overton - 3,3',5'-triiodothyronine concentration assay + + + DNase Hi-C assay + + A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts. + Michelle Giglio + Suvarna Nadendla + EFO:0009976 + PMID:27685100 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + DNase Hi-C assay - + - - - A fibrinogen assay that measures the concentration of fibrinogen in a specimen. - James A. Overton - fibrinogen concentration assay + + + micro-C assay + + A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step. + Michelle Giglio + Suvarna Nadendla + EFO:0008808 + PMID:26119342 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + micro-C assay - + - - - A thyroxine assay that measures the concentration of free thyroxine in a specimen. - James A. Overton - free thyroxine concentration assay + + + single cell combinatorial indexing Hi-C assay + + A Hi-C assay performed on massively multiplexed single-cell samples. + Michelle Giglio + Suvarna Nadendla + sci-Hi-C + EFO:0009977 + PMID:28135255 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + single cell combinatorial indexing Hi-C assay - + - - - A thyroxine assay that measures the concentration of total thyroxine in a specimen. - James A. Overton - total thyroxine concentration assay + + + single nucleus Hi-C assay + + A Hi-C assay performed on isolated nuclei. + Michelle Giglio + Suvarna Nadendla + sn-Hi-C + EFO:0009978 + PMID:28355183 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + single nucleus Hi-C assay - + - - - A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen. - James A. Overton - direct bilirubin concentration assay + + + single cell Hi-C assay + + A Hi-C assay performed on a single cell. + Michelle Giglio + Suvarna Nadendla + EFO:0009979 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + single cell Hi-C assay - + - - - A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen. - James A. Overton - indirect bilirubin concentration assay + + + bulk Hi-C assay + + A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. + Michelle Giglio + Suvarna Nadendla + 4DN DCIC + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + bulk Hi-C assay - + - - - A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen. - James A. Overton - total bilirubin concentration assay + + + multi-contact Hi-C assay + + A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read library is produced in which many ligated fragments may be contained in a single molecule. The library is then sequenced on a long read sequencer. + Michelle Giglio + Suvarna Nadendla + MC-3C + MC-HI-C + The 4D Nucleome Network + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + multi-contact Hi-C assay - + - - - A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes. - James A. Overton - mean cell hemoglobin assay + + + transposase-mediated analysis of chromatin looping assay + + A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions. + Michelle Giglio + Suvarna Nadendla + TrAC-Loop + EFO:0009982 + PMID:30150754 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + transposase-mediated analysis of chromatin looping assay - + - - - A hemoglobin assay that measures the concentration of hemoglobin in a specimen. - James A. Overton - mean cell hemoglobin concentration assay + + + split-pool recognition of interactions and tag extension assay + + A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed. + Michelle Giglio + Suvarna Nadendla + SPRITE + EFO:0009984 + PMID:29887377 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + split-pool recognition of interactions and tag extension assay - + - - - A platelet assay that measures the average volume of platelets in a specimen. - James A. Overton - mean platelet volume assay + + + DNA split-pool recognition of interactions and tag extension assay + + A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA. + Michelle Giglio + Suvarna Nadendla + DNA SPRITE + EFO:0009985 + PMID:29887377 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + DNA split-pool recognition of interactions and tag extension assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A neutrophil assay that measures the number of immature neutrophils in a specimen. - James A. Overton - immature neutrophil count assay + + + RNA-DNA split-pool recognition of interactions and tag extension assay + + A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions. + Michelle Giglio + Suvarna Nadendla + RNA-DNA SPRITE + EFO:0009986 + PMID:29887377 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + RNA-DNA split-pool recognition of interactions and tag extension assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An neutrophil assay that measures the percentage of immature neutrophils in a specimen. - James A. Overton - immature neutrophil percentage assay + + + genome architecture mapping assay + + A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput sequencing, and subsequent analysis can generate a matrix of inferred proximity between genomic regions. + Michelle Giglio + Suvarna Nadendla + GAM + EFO:0009987 + PMID:28273065 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + genome architecture mapping assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - - - - + + + + + + - An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen. - James A. Overton - nucleated erythrocyte percentage assay - - - - - - - - - An erythrocyte assay that measures the average volume of erythrocytes in a specimen. - James A. Overton - mean cell volume assay + mapping RNA-genome interactions assay + + A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed. + Michelle Giglio + Suvarna Nadendla + MARGI + EFO:0009988 + PMID:28132817 + https://github.com/obi-ontology/obi/issues/1472 + CFDE-4DN + mapping RNA-genome interactions assay - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - A cytometry assay that measures the abundance and/or characteristics of erythrocytes. - James A. Overton - erythrocyte assay + + + + assay measuring epitope specific amphiregulin production by T cells + + A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells. + IEDB + IEDB + amphiregulin release|biological activity + assay measuring epitope specific amphiregulin production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes. - James A. Overton - manual hematocrit assay + + ELISA measuring epitope specific amphiregulin production by T cells + + An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells. + IEDB + IEDB + amphiregulin release|ELISA + ELISA measuring epitope specific amphiregulin production by T cells - + - - + + - - - - - - - - - - - - - - - - + + - An analyte assay that measures the abundance of adiponectin - James A. Overton - adiponectin assay + perforin release during T cell degranulation + + The release of perforin during cytotoxic T cell degranulation. + Bjoern Peters + Hector Guzman-Orozco + Alexander Diehl, Bjoern Peters + perforin release during T cell degranulation - + - - + + - - - - - - - - - - - - - - - - + + - An adiponectin assay that measures the concentration of adiponectin in a specimen. - James A. Overton - adiponectin concentration assay + granzyme A release during T cell degranulation + + The release of granzyme A during cytotoxic T cell degranulation. + Bjoern Peters + Hector Guzman-Orozco + Alexander Diehl, Bjoern Peters + granzyme A release during T cell degranulation - + - - + + - - - - - - - - - - - - - - - - + + - An analyte assay that measures the abundance of creatine - James A. Overton - creatine assay + granzyme B release during T cell degranulation + + The release of granzyme B during cytotoxic T cell degranulation. + Bjoern Peters + Hector Guzman-Orozco + Alexander Diehl, Bjoern Peters + granzyme B release during T cell degranulation - + - - + + - - - - - - - - - - - - - - - - + + - A creatine assay that measures the concentration of creatine in a specimen. - James A. Overton - creatine concentration assay + granulysin release during T cell degranulation + + The release of granulysin during cytotoxic T cell degranulation. + Bjoern Peters + Hector Guzman-Orozco + Alexander Diehl, Bjoern Peters + granulysin release during T cell degranulation - + - - + + @@ -76514,10 +93597,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -76525,57 +93608,21 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - An analyte assay that measures the abundance of estradiol - James A. Overton - estradiol assay - - - - - - - - - - - - - - + - - + + - - - - - An estradiol assay that measures the concentration of estradiol in a specimen. - James A. Overton - estradiol concentration assay - - - - - - - - @@ -76584,10 +93631,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -76595,173 +93642,341 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - An analyte assay that measures the abundance of leptin - James A. Overton - leptin assay + venous blood microbiology assay + + A blood microbiology assay that identifies a microorganism in a venous blood specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1491 + venous blood microbiology assay - + - - - An leptin assay that measures the concentration of leptin in a specimen. - James A. Overton - leptin concentration assay + + + high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex + Next-generation high-density peptide microarrays measuring antibody responses to overlapping peptides: PMID:25922409. + + A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay. + IEDB + IEDB + antibody binding|High throughput multiplexed assay + high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex - + - - + + + high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex + Adaptive Biotech multiplexed TCR sequencing assays: PMID:32793919. + + A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay. + IEDB + IEDB + T cell binding|High throughput multiplexed assay + high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex + + + + + + + + + high throughput multiplexed assay measuring binding of a MHC:ligand complex + Peptide microarray with fluorescence detection for millions of MHC binding measurements: PMID: 33705522. + + A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay. + IEDB + IEDB + MHC binding|High throughput multiplexed assay + high throughput multiplexed assay measuring binding of a MHC:ligand complex + + + + + + + + + high throughput multiplexed assay measuring MHC ligand processing and presentation + Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands witth a false discovery rate: PMID: 29789417. + + A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay. + IEDB + IEDB + ligand presentation|High throughput multiplexed assay + high throughput multiplexed assay measuring MHC ligand processing and presentation + + + + + + + + + + + + + + + milk assay datum + + A data item that is the specified output of a milk assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1515 + milk assay datum + + + + + + + + + + + + + + + organism diagnostic process + + A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has a disease, disorder, or syndrome of a certain type, or none of these as output. + Jie Zheng + https://github.com/obi-ontology/obi/issues/1505 + organism diagnostic process + + + + + + + + + + + + + + + diagnosis of an organism + + A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. + Jie Zheng + https://github.com/obi-ontology/obi/issues/1505 + diagnosis of an organism + + + + + + + + + + + + + + detection technique + Using a radioactivity detection assay as part of a tritiated thymidine incorporation assay to determine the degree to which cells are replicating by detecting radioactivity of tritiated thymidine, where radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. + + An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B. + Bjoern Peters + Hector Guzman-Orozco + OBI + https://github.com/obi-ontology/obi/issues/1488 + detection technique + + + + + + + + + assay kit + Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf + + A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. + John Judkins + OBI, VEuPathDB + https://github.com/obi-ontology/obi/issues/1456 + VEuPathDB + assay kit + + + + + + + + + - - - - - - - - - - - - - - - - + + - - An analyte assay that measures the abundance of lipoprotein - James A. Overton - lipoprotein concentration assay + + + epitope specific XCL1 release by T cells + + A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope. + IEDB + IEDB + epitope specific XCL1 release by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen. - James A. Overton - high-density lipoprotein concentration assay + + assay measuring epitope specific lymphotactin production by T cells + + A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells. + IEDB + IEDB + lymphotactin release|biological activity + assay measuring epitope specific lymphotactin production by T cells - + - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen. - James A. Overton - low-density lipoprotein concentration assay + + ELISA measuring epitope specific lymphotactin production by T cells + + An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells. + IEDB + IEDB + lymphotactin release|ELISA + ELISA measuring epitope specific lymphotactin production by T cells - + - - - + + + remote patient assessment + A telephone or video remote patient assessment conducted between a physician and patient. + + An organism diagnostic process which involves a remote assessment of a patient by a clinician. + + telehealth patient assessment + + 2022-05-02T14:15:39Z + remote patient assessment + + + + + + + + + - - - - - - - - - - - - + + - - + + - - A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen. - James A. Overton - very-low-density lipoprotein concentration assay + + placental blood specimen + + A specimen that is derived from placental blood. + John Judkins + VEuPathDB + placental blood specimen - + - - + + @@ -76770,10 +93985,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -76781,550 +93996,667 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - An analyte assay that measures the abundance of luteinizing hormone - James A. Overton - luteinizing hormone assay - - - - - - - - - A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen. - James A. Overton - luteinizing hormone concentration assay - - - - - - - - - - - - - - + - - + + - - - - - An analyte assay that measures the abundance of nitrite - James A. Overton - nitrite assay + placental blood microbiology assay + + A blood microbiology assay that has a placental blood specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1297 + placental blood microbiology assay - + - - - A nitrite assay that measures the concentration of nitrite in a specimen. - James A. Overton - nitrite concentration assay + + + + + + + + + placental blood microbiology datum + + An organism identification datum that is the specified output of a placental blood microbiology assay. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1297 + placental blood microbiology datum - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - An analyte assay that measures the abundance of phospholipid - James A. Overton - phospholipid assay + eukaryota in placental blood datum + + A placental blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1297 + eukaryota in placental blood datum - + - - - A phospholipid assay that measures the concentration of phospholipids in a specimen. - James A. Overton - phospholipid concentration assay + + + synaptosome preparation process + + A material component separation process where a synaptic terminal is isolated from a neuron by mild homogenization of nervous tissue under isotonic conditions and subsequent fractionation using differential and density gradient centrifugation. + Michelle Giglio + Suvarna Nadendla + url:https://en.wikipedia.org/wiki/Synaptosome + CFDE-GlyGen + synaptosome preparation process - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - An analyte assay that measures the abundance of progesterone - James A. Overton - progesterone assay + Illumina HiSeq 1500 + + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + HiSeq 1500 + https://jp.support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Illumina HiSeq 1500 - + - - - A progesterone assay that measures the concentration of progesterone in a specimen. - James A. Overton - progesterone concentration assay + + + + + + + + + NextSeq 550 + + A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.illumina.com/systems/sequencing-platforms/nextseq.html + https://github.com/obi-ontology/obi/issues/1546 + gEAR + NextSeq 550 - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - An analyte assay that measures the abundance of testosterone - James A. Overton - testosterone assay + Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 + + A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.agilent.com/cs/library/brochures/IBS-231%20genomics%20catalog%20mech%20FINAL.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 - + - - - A testosterone assay that measures the concentration of testosterone in a specimen. - James A. Overton - testosterone concentration assay + + + + + + + + + Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray + + A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.agilent.com/cs/library/brochures/5990-6928en_lo.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - An analyte assay that measures the abundance of bile salt - James A. Overton - bile salt assay + Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray + + A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.agilent.com/cs/library/usermanuals/public/G4140-90050_GeneExpression_TwoColor_6.9.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray - + - - - A bile salt assay that measures the concentration of bile salt in a specimen. - James A. Overton - bile salt concentration assay + + + + + + + + + Affymetrix Mouse Genome 430 2.0 Array + + A DNA microarray manufactured by Affymetrix, which includes complete coverage of the GeneChip Mouse Expression Set 430, for analysis of over 39,000 transcripts and variants from more than 34,000 well-characterized mouse genes and UniGene clusters, on a single array. The sequences for this array were selected from GenBank™, dbEST, and RefSeq., and sequence clusters cretaed from the UniGene database. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Mouse Genome 430 2.0 Array + https://www.thermofisher.com/order/catalog/product/900497 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Genome 430 2.0 Array - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - An analyte assay that measures the abundance of fatty acid - James A. Overton - fatty acid assay + Affymetrix Mouse Genome 430A 2.0 Array + + A DNA microarray manufactured by Affymetrix for gene expression analysis focusing on approximately 14,000 well-characterized genes in the transcribed mouse genome using single-array cartridge. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Mouse Genome 430A 2.0 Array + https://www.thermofisher.com/order/catalog/product/900500TS?SID=srch-srp-900500TS + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Genome 430A 2.0 Array - + - - - A fatty acid assay that measures the concentration of free fatty acids in a specimen. - James A. Overton - free fatty acid concentration assay + + + + + + + + + Affymetrix Mouse Gene 1.0 ST Array + + A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Mouse Gene 1.0 ST Array + https://www.thermofisher.com/order/catalog/product/901168 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Gene 1.0 ST Array - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - An analyte assay that measures the abundance of insulin - James A. Overton - insulin assay + Affymetrix Mouse Gene 2.1 ST Array + + A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA).To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Mouse Gene 2.1 ST Array + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fmouse_gene_array_datasheet.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Gene 2.1 ST Array - + - - - A insulin assay that measures the concentration of insulin in a specimen. - James A. Overton - insulin concentration assay + + + + + + + + + Affymetrix Rhesus Macaque Genome Array + + A DNA microarray manufactured by Affymetrix,which is a single-labeled high-density oligonucleotide array, designed to study gene expression in the rhesus animal model and to interrogate rhesus transcripts orthologous to the 3' end of human transcripts. The array consists of over 52,000 probe sets representing more than 20,000 genes, and several relevant viral organisms for studying host-disease immune response. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Rhesus Macaque Genome Array + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0017705_702023_RhesusArray_PI.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Rhesus Macaque Genome Array - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - An analyte assay that measures the abundance of follicle stimulating hormone - James A. Overton - follicle stimulating hormone assay + Affymetrix Human Transcriptome Array 2.0 + + A DNA microarray manufactured by Affymetrix, to go beyond gene-level expression profiling to accurately detect all known transcript isoforms produced by a gene. The array design covers >245,000 coding transcripts, >40,000 non-coding transcripts and >339,000 probe sets covering exon-exon junctions, thus ensuring uniform coverage of the transcriptome. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Human Transcriptome Array 2.0 + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fhta_array_2_0_datasheet.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Human Transcriptome Array 2.0 - + - - - A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen. - James A. Overton - follicle stimulating hormone concentration assay + + + + + + + + + Affymetrix Human Genome U219 Array + + A DNA microarray manufactured by Affymetrix, which comprises more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + Applied Biosystems GeneChip PrimeView Human Gene Expression Array + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0017681_703036_GeneChipPrimeViewArray_PI.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Human Genome U219 Array - + - - - A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen. - James A. Overton - total lymphocyte count assay + + + + + + + + + Affymetrix Human Gene 2.0 ST Array + + A DNA microarray manufactured by Affymetrix, which provides the most accurate, sensitive, and comprehensive measurement of protein coding (mRNA) and long intergenic non-coding RNA (lincRNA) transcripts. The array design covers >33,500 coding transcripts and >11,000 lincRNA transcripts thus enabling researchers to understand whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + GeneChip Human Gene 2.0 ST Array + https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fhugene_2_st_datasheet.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Human Gene 2.0 ST Array - + - - - A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen. - James A. Overton - total lymphocyte percentage assay + + + + + + + + + Affymetrix Clariom S Assay, Human + + A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the human transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers , and to quickly assess changes in key genes and pathways. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.thermofisher.com/order/catalog/product/902926#1_1 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Clariom S Assay, Human - + - - + + - - - - - - - - - + + - A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies. - Hector Guzman-Orozco - FLUOROSPOT - https://en.wikipedia.org/wiki/ELISpot#Mechanism_of_FluoroSpot - https://github.com/obi-ontology/obi/issues/1414 - CMI-PB - fluorescent immunospot assay + Affymetrix Clariom S Assay, Mouse + + A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the mouse transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers, and to quickly assess changes in key genes and pathways. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.thermofisher.com/order/catalog/product/902931?SID=srch-srp-902931, + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Clariom S Assay, Mouse - + - - + + - - + + - A proteomics profiling assay that detects proteins in a blood plasma specimen. - Hector Guzman-Orozco - CMI-PB - https://github.com/obi-ontology/obi/issues/1414 - CMI-PB - plasma proteomics assay + Illumina HumanHT-12 V4.0 expression beadchip + + An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling and expression-based quantitative trait loci (eQTL) studies. This BeadChip contains 12 arrays, each featuring more than 48,000 probes, targeting more than 31,000 annotated genes, providing genome-wide coverage of well-characterized genes, gene candidates, and splice variants. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://www.illumina.com/documents/products/technotes/technote_humanht_12_imputation.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Illumina HumanHT-12 V4.0 expression beadchip - + - - - A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers. - Hector Guzman-Orozco - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4955771/ - https://github.com/obi-ontology/obi/issues/1414 - CMI-PB - T cell activation induced marker assay + + + + + + + + + Illumina MouseRef-8 v2.0 beadchip + + An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling in the mouse.This Beadchip contains 8 microarrays, featuring more than 25,000 probes per array, derived from the NCBI RefSeq database and supplemented with MEEBO and RIKEN FANTOM2 content. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/arraykits/whole-genome-gene-expression/WGGEX_Direct_Hybridization_Assay_Guide_11322355_A.pdf, https://www.illumina.com/documents/products/datasheets/datasheet_gene_exp_analysis.pdf + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Illumina MouseRef-8 v2.0 beadchip - + - - + + - - + + - A blood harvesting process in which white blood cells are separated from a blood specimen. - Hector Guzman-Orozco - https://en.wikipedia.org/wiki/Leukapheresis - leukapheresis + Affymetrix Mouse Exon Junction Array + + A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the mouse transcriptome. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://academic.oup.com/bioinformatics/article/26/2/268/209989 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Mouse Exon Junction Array - + - - + + + + + + + + + Affymetrix Human Exon Junction Array + + A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the human transcriptome. + Jain Aluvathingal + Michelle Giglio + Suvarna Nadendla + https://academic.oup.com/bioinformatics/article/26/2/268/209989 + https://github.com/obi-ontology/obi/issues/1546 + gEAR + Affymetrix Human Exon Junction Array + + + + + + + + + administering substance in vivo to cause disease + + An administration of substance in vivo with the intention to induce disease in the organism. + IEDB + IEDB + administering substance in vivo to cause disease + + + + + + + + + administering substance in vivo to reduce or prevent disease + + An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. + IEDB + IEDB + administering substance in vivo to reduce or prevent disease + + + + + + + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - An assay that has a cerebrospinal fluid specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - cerebrospinal fluid assay + peripheral blood mononuclear cell specimen + + A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. + Chris Stoeckert + Jie Zheng + PBMC specimen + http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell + peripheral blood mononuclear cell specimen + + + + + + + + + + + + + + + + + + + + + + + + + mid-upper arm circumference datum + + A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm. + The Mother and Child Health and Education Trust + mid-upper arm circumference datum + + + + + + + + + + + + + + + antigen specific antibodies assay datum + + A data item that is the specified output of an antigen specific antibodies assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + antigen specific antibodies assay datum - + - - + + @@ -77336,7 +94668,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -77347,7 +94679,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -77359,19 +94691,22 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An assay that has an endotracheal aspirate specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - endotracheal aspirate assay + antigen specific antibodies in blood assay + + An antigen specific antibodies assay that has a blood specimen as evaluant. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + VEuPathDB + antigen specific antibodies in blood assay - + - - + + @@ -77383,7 +94718,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -77394,7 +94729,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -77406,1530 +94741,1969 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An assay that has an induced sputum specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - induced sputum assay + antigen specific antibodies in milk assay + + An antigen specific antibodies assay that has a milk specimen as evaluant. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + VEuPathDB + antigen specific antibodies in milk assay - + - + + + + + + + + + antigen specific antibodies in blood assay datum + + An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + antigen specific antibodies in blood assay datum + + + + + + + + + + + + + + + antigen specific antibodies in milk assay datum + + An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1526 + antigen specific antibodies in milk assay datum + + + + + + + - - - - - - - - - - - - - - - - + + + - - - - - - - - - - - - + + - - + + - An assay that has a lung specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - lung assay + enzymatic activity level assay + + An assay in which the level of catalytic activity of an enzyme is determined. + James A. Overton + enzymatic activity level assay - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + - - An assay that has a milk specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - milk assay + + 5'-nucleotidase activity level assay + + An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample. + James A. Overton + 5'-nucleotidase activity level assay - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + - - An assay that has a feces specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - feces assay + + alanine aminotransferase activity level assay + + An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample. + James A. Overton + alanine aminotransferase activity level assay - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + - - An assay that has an umbilical cord blood specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - umbilical cord blood assay + + alkaline phosphatase activity level assay + + An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample. + James A. Overton + alkaline phosphatase activity level assay - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + - - An assay that has a saliva specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - saliva assay + + amylase activity level assay + + An enzymatic activity level assay that measures the activity of amylase in a sample. + James A. Overton + amylase activity level assay - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + - - An organism identification assay that has a cerebrospinal fluid specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - cerebrospinal fluid microbiology assay + + aspartate aminotransferase activity level assay + + An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample. + James A. Overton + aspartate aminotransferase activity level assay - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + - - An organism identification assay that has an endotracheal aspirate specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - endotracheal tube aspirate microbiology assay + + cholinesterase activity level assay + + An enzymatic activity level assay that measures the activity of cholinesterase in a sample. + James A. Overton + cholinesterase activity level assay - + - - - + + + - - - - - - - - - - - - - - - + - - - - - - - - - + + + + - - An organism identification assay that has an induced sputum specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - induced sputum microbiology assay - - - - - - - - - - - - - - - A data item that is the specified output of a blood assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - blood assay datum - - - - - - - - - - - - - - - An organism identification assay that is the specified output of a blood microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - blood microbiology datum - - - - - - - - - - - - - - - A data item that is the specified output of a feces assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - feces assay datum - - - - - - - - - - - - - - - An organism identification assay that is the specified output of a feces microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - feces microbiology datum - - - - - - - - - - - - - - - A data item that is the specified output of a urine assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - urine assay datum - - - - - - - - - - - - - - - An organism identification assay that is the specified output of a urine microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - urine microbiology datum - - - - - - - - - - - - - - - A data item that is the specified output of a induced sputum assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - induced sputum assay datum + + creatine kinase activity level assay + + An enzymatic activity level assay that measures the activity of creatine kinase in a sample. + James A. Overton + creatine kinase activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of an induced sputum microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - induced sputum microbiology datum + + + + + + + + + + + + + + + + + + gamma-glutamyltransferase activity level assay + + An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample. + James A. Overton + gamma-glutamyltransferase activity level assay - + - - - - - - - - - A data item that is the specified output of a cerebrospinal fluid assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - cerebrospinal fluid assay datum + + + + + + + + + + + + + + + + + + glutamate dehydrogenase activity level assay + + An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample. + James A. Overton + glutamate dehydrogenase activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of a cerebrospinal fluid microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - cerebrospinal fluid microbiology datum + + + + + + + + + + + + + + + + + + isocitrate dehydrogenase activity level assay + + An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample. + James A. Overton + isocitrate dehydrogenase activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of an endotracheal aspirate assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - endotracheal aspirate assay datum + + + + + + + + + + + + + + + + + + lactate dehydrogenase activity level assay + + An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample. + James A. Overton + lactate dehydrogenase activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of an endotracheal tube aspirate microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - endotracheal tube aspirate microbiology datum + + + + + + + + + + + + + + + + + + sorbitol dehydrogenase activity level assay + + An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. + James A. Overton + sorbitol dehydrogenase activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of a lung microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - lung microbiology datum + + + + + + + + + + + + + + + + + + acyl-CoA oxidase activity level assay + + An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. + James A. Overton + acyl-CoA oxidase activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - nasopharyngeal or oropharyngeal swab microbiology datum + + + + + + + + + + + + + + + + + + N-acetyl-beta-glucosaminidase activity level assay + + An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. + James A. Overton + N-acetyl-beta-glucosaminidase activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of a pleural fluid microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - pleural fluid microbiology datum + + + + + + + + + + + + + + + + + + ribonuclease activity level assay + + An enzymatic activity level assay that measures the activity of ribonuclease in a sample. + James A. Overton + ribonuclease activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of an umbilical cord blood assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - umbilical cord blood assay datum + + + + + + + + + + + + + + + + + + galactosidase activity level assay + + An enzymatic activity level assay that measures the activity of galactosidase in a sample. + James A. Overton + galactosidase activity level assay - + - - - - - - - - - An organism identification assay that is the specified output of an umbilical cord blood microbiology assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - umbilical cord blood microbiology datum + + + Mosquito Magnet Liberty Plus trap + + An arthropod trap that is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor. + VEuPathDB + https://github.com/obi-ontology/obi/issues/1523 + Mosquito Magnet Liberty Plus trap - + - - + + - - + + + + + + + + + + + + - A blood microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - bacteria in blood datum - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - A blood microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - virus in blood datum + tumor challenge + + The administration of a malignant cell to a host. + Hector Guzman-Orozco + IEDB + tumor challenge - + - - - - - - - - - A blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - eukaryota in blood datum + + + in vivo challenge + + The administration of a challenge to a live host. + Hector Guzman-Orozco + IEDB + in vivo challenge - + - - - - - - - - - A feces microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - bacteria in feces datum + + + epitope protection from infectious challenge experiment based on survival + + An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. + Hector Guzman-Orozco + survival after infectious challenge + IEDB + https://github.com/obi-ontology/obi/issues/1594 + epitope protection from infectious challenge experiment based on survival - + - - - - - - - - - A feces microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - eukaryota in feces datum + + + epitope protection from tumor challenge experiment based on burden + + An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls. + Hector Guzman-Orozco + burden after tumor challenge + IEDB + https://github.com/obi-ontology/obi/issues/1594 + epitope protection from tumor challenge experiment based on burden - + - - - - - - - - - A feces microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - virus in feces datum + + + epitope protection from tumor challenge experiment based on survival + + An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. + Hector Guzman-Orozco + survival after tumor challenge + IEDB + https://github.com/obi-ontology/obi/issues/1594 + epitope protection from tumor challenge experiment based on survival - + - - - - - - - - - A urine microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - eukaryota in urine datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from pathogen challenge + + An in vivo assay measuring T cell epitope specific protection from pathogen challenge. + IEDB + IEDB + protection from pathogen challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection from pathogen challenge - + - - - - - - - - - A induced sputum microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - bacteria in induced sputum datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from tumor challenge + + An in vivo assay measuring T cell epitope specific protection from tumor challenge. + IEDB + IEDB + protection from tumor challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection from tumor challenge - + - - - - - - - - - A induced sputum microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - eukaryota in induced sputum datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from other challenge + + An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor. + IEDB + IEDB + protection from other challenge|in vivo assay + in vivo assay measuring T cell epitope specific protection from other challenge - + - - - - - - - - - A induced sputum microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - virus in induced sputum datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific survival after tumor challenge + + An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival. + IEDB + IEDB + survival from tumor challenge|in vivo assay + in vivo assay measuring T cell epitope specific survival after tumor challenge - + - - - - - - - - - A endotracheal tube aspirate microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - bacteria in endotracheal tube aspirate datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific survival after pathogen challenge + + An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival. + IEDB + IEDB + survival from pathogen challenge|in vivo assay + in vivo assay measuring T cell epitope specific survival after pathogen challenge - + - - - - - - - - - A lung microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - bacteria in lung datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from pathogen challenge + + An in vivo assay measuring B cell epitope specific protection from pathogen challenge. + IEDB + IEDB + protection from pathogen challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection from pathogen challenge - + - - - - - - - - - A lung microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - eukaryota in lung datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from tumor challenge + + An in vivo assay measuring B cell epitope specific protection from tumor challenge. + IEDB + IEDB + protection from tumor challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection from tumor challenge - + - - - - - - - - - A lung microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - virus in lung datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from other challenge + + An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor. + IEDB + IEDB + protection from other challenge|in vivo assay + in vivo assay measuring B cell epitope specific protection from other challenge - + - - - - - - - - - A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - bacteria in nasopharyngeal or oropharyngeal swab datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific survival after pathogen challenge + + An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival. + IEDB + IEDB + survival from pathogen challenge|in vivo assay + in vivo assay measuring B cell epitope specific survival after pathogen challenge - + - - - - - - - - - A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - eukaryota in nasopharyngeal or oropharyngeal swab datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific survival after tumor challenge + + An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival. + IEDB + IEDB + survival from tumor challenge|in vivo assay + in vivo assay measuring B cell epitope specific survival after tumor challenge - + - - - - - - - - - A nasopharyngeal or oropharyngeal swab microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - virus in nasopharyngeal or oropharyngeal swab datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells + + An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from pathogen challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells - + - - + + - - + + - A pleural fluid microbiology datum that is interpreted as an indication of the presence of bacteria in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - bacteria in pleural fluid datum - - - - - - - - - - + + + + + + + + + - A pleural fluid microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - eukaryota in pleural fluid datum - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - A pleural fluid microbiology datum that is interpreted as an indication of the presence of viruses in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - virus in pleural fluid datum - - - - - - - - - - + + + + + + + + + + + + - A umbilical cord blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1428 - eukaryota in umbilical cord blood datum + in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival. + IEDB + IEDB + survival after pathogen challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival - + - - - + + + - + + + + + + + + + - - - + + + - - + + + + + + + + + + + + - - + + - + - - - + + + - - + + - - + + - - An organism identification assay that has a lung specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - lung microbiology assay + + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells + + An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells. + IEDB + IEDB + protection from tumor challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells - + - - + + - - + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + + + - - + + - An organism identification assay that has a pleural fluid specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - pleural fluid microbiology assay + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival + + An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival. + IEDB + IEDB + survival after tumor challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival - + - - - + + + - + + + + + - - + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + - + - - - + + + - - + + - - + + - - An organism identification assay that has an umbilical cord blood specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - umbilical cord blood microbiology assay + + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells + + An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells. + IEDB + IEDB + protection from other challenge after adoptive transfer|in vivo assay + in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells - + - - - + + + - + + + + + + + + + - - - + + + - + - - - - + + + + + + + - - + + - + - - - - - - - - + + + - - + + - - + + - - An organism identification assay that has a nasopharyngeal or oropharyngeal swab specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - nasopharyngeal or oropharyngeal swab microbiology assay + + in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from pathogen challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells - + - - + + - - + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + + + - - + + - An organism identification assay that has a urine specimen as evaluant. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1429 - urine microbiology assay - - - - - - - - - A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. - John Judkins - multiplexed real time polymerase chain reaction assay - VEuPathDB - https://github.com/obi-ontology/obi/issues/1431 - multiplex real time polymerase chain reaction assay - - - - - - - - - A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. - John Judkins - multiplexed real time reverse-transcription polymerase chain reaction assay - VEuPathDB - https://github.com/obi-ontology/obi/issues/1431 - multiplex real time reverse-transcription polymerase chain reaction assay - - - - - - - - - A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1439 - mosquito membrane feeding device + in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. + IEDB + IEDB + survival after pathogen challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival - + - - - + + + - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - + + - + - - - + + + - - + + + + + + + + + + + + - - + + - - - - - - - + - - - + + + - - + + - - + + - - - - - - Testing the effectiveness of drugs or antibodies against parasite transmission. - An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1439 - mosquito membrane feeding assay - - - - - - - - - A study design that is executed primarily on a computer. - Hector Guzman-Orozco - https://en.wikipedia.org/wiki/In_silico - https://github.com/obi-ontology/obi/issues/1430 - CMI-PB - in silico design + + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from tumor challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells - + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - + - + - + - - + + @@ -78937,40 +96711,96 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - A cytometric bead array assay that detects epitope specific granulysin release by T cells. - IEDB - IEDB - granulysin release|cytometric bead array - cytometric bead array assay measuring epitope specific granulysin release by T cells + + + + + + + + + + + + + + + + + + + + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival + + An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. + IEDB + IEDB + survival after tumor challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + + + + @@ -78978,126 +96808,119 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A cytometric bead array assay that detects epitope specific perforin release by T cells. - IEDB - IEDB - perforin release|cytometric bead array - cytometric bead array assay measuring epitope specific perforin release by T cells + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + + An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells. + IEDB + IEDB + protection from other challenge after adoptive transfer|in vivo assay + in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells - + - - - - - - - - - A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. - John Judkins - NCIT:C85736 - https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html - https://github.com/obi-ontology/obi/issues/1444 - modified acid-fast stain microscopy assay + + + Gram stain assay + + An organism identification assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall. + Gram-positive bacteria retain the violet stain whereas gram-negative bacteria do not. + John Judkins ORCID:0000-0001-6595-0902 + American Heritage Medical Dictionary + NCI + https://github.com/obi-ontology/obi/issues/1603 + Gram stain assay - + - - - A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. - Bjoern Peters - Hector Guzman-Orozco - IEDB - positive binding datum + + + + + + + + + cow-baited arthropod trap + + A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent. + John Judkins ORCID:0000-0001-6595-0902 + Sarah Kelly + https://github.com/obi-ontology/obi/issues/1602 + cow-baited arthropod trap - + - - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + + lymph specimen + + A specimen that is derived from a portion of lymph collected from an organism. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + lymph specimen + + + + + + + + - - - - - - - - - - - - + + - - + + + + + + + - PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes. - An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. - John Judkins - ALS assay - antibodies from lymphocyte supernatant assay - OBI - VEuPathDB - https://github.com/obi-ontology/obi/issues/1443 - antibodies from lymphocyte secretions assay + digestive tract specimen + + A specimen that is derived from part of a digestive tract. + John Judkins ORCID:0000-0001-6595-0902 + VEuPathDB + digestive tract specimen - + - + @@ -79110,7 +96933,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -79124,22 +96947,24 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells. - IEDB - IEDB - amphiregulin release|biological activity - assay measuring epitope specific amphiregulin production by T cells + assay measuring epitope specific interleukin-25 production by T cells + + A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells. + IEDB + IEDB + IL-25 release|biological activity + assay measuring epitope specific interleukin-25 production by T cells - + - + - + @@ -79148,7 +96973,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -79162,335 +96987,133 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells. - IEDB - IEDB - amphiregulin release|ELISA - ELISA measuring epitope specific amphiregulin production by T cells - - - - - - - - - - - - - - - - - - - The release of perforin during cytotoxic T cell degranulation. - Bjoern Peters - Hector Guzman-Orozco - Alexander Diehl, Bjoern Peters - perforin release during T cell degranulation - - - - - - - - - - - - - - - - - - - The release of granzyme A during cytotoxic T cell degranulation. - Bjoern Peters - Hector Guzman-Orozco - Alexander Diehl, Bjoern Peters - granzyme A release during T cell degranulation + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells + + A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells. + IEDB + IEDB + IL-25 release|RNA/DNA detection + detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells - + - - + + - + - - + + + + + + + + + + + + + + + + + - - The release of granzyme B during cytotoxic T cell degranulation. - Bjoern Peters - Hector Guzman-Orozco - Alexander Diehl, Bjoern Peters - granzyme B release during T cell degranulation + + intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells + + A flow cytometry assay that detects interleukin-25 production by T cells. + IEDB + IEDB + IL-25 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells - + - - + + - + - - + + + + + + + + + + + + + + + + + - - The release of granulysin during cytotoxic T cell degranulation. - Bjoern Peters - Hector Guzman-Orozco - Alexander Diehl, Bjoern Peters - granulysin release during T cell degranulation + + ELISA measuring epitope specific interleukin-25 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells. + IEDB + IEDB + IL-25 release|ELISA + ELISA measuring epitope specific interleukin-25 production by T cells - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + - + - - - - - - - - - + + + + + + + + + + + + + + - - - - - - A blood microbiology assay that identifies a microorganism in a venous blood specimen. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1491 - venous blood microbiology assay - - - - - - - - - Next-generation high-density peptide microarrays measuring antibody responses to overlapping peptides: PMID:25922409. - A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay. - IEDB - IEDB - antibody binding|High throughput multiplexed assay - high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex - - - - - - - - - Adaptive Biotech multiplexed TCR sequencing assays: PMID:32793919. - A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay. - IEDB - IEDB - T cell binding|High throughput multiplexed assay - high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex - - - - - - - - - Peptide microarray with fluorescence detection for millions of MHC binding measurements: PMID: 33705522. - A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay. - IEDB - IEDB - MHC binding|High throughput multiplexed assay - high throughput multiplexed assay measuring binding of a MHC:ligand complex - - - - - - - - - Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands witth a false discovery rate: PMID: 29789417. - A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay. - IEDB - IEDB - ligand presentation|High throughput multiplexed assay - high throughput multiplexed assay measuring MHC ligand processing and presentation - - - - - - - - - - - - - - - A data item that is the specified output of a milk assay. - John Judkins - VEuPathDB - https://github.com/obi-ontology/obi/issues/1515 - milk assay datum - - - - - - - - - - - - - - - A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has a disease, disorder, or syndrome of a certain type, or none of these as output. - Jie Zheng - https://github.com/obi-ontology/obi/issues/1505 - organism diagnostic process - - - - - - - - - - - - - - - A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. - Jie Zheng - https://github.com/obi-ontology/obi/issues/1505 - diagnosis of an organism - - - - - - - - - - - - - - - Using a radioactivity detection assay as part of a tritiated thymidine incorporation assay to determine the degree to which cells are replicating by detecting radioactivity of tritiated thymidine, where radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. - An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B. - Bjoern Peters - Hector Guzman-Orozco - OBI - https://github.com/obi-ontology/obi/issues/1488 - detection technique - - - - - - - - - assay kit - Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf - A processed material that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. - John Judkins - OBI, VEuPathDB - assay kit - - - - - - - - - A telephone or video remote patient assessment conducted between a physician and patient. - An organism diagnostic process which involves a remote assessment of a patient by a clinician. - - telehealth patient assessment - - 2022-05-02T14:15:39Z - remote patient assessment + + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + + A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells. + IEDB + IEDB + TNF release|bioassay + cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -79499,13 +97122,13 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - injection function + injection function - The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - adapted from WEB: http://www.dictionary.net/injection - injection function + The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + adapted from WEB: http://www.dictionary.net/injection + injection function @@ -79542,8 +97165,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch Epstein Barr virus transformed B cell @@ -79567,15 +97190,16 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - Tissue, organ, system, sperm, blood or body location (arm). + obsolete_anatomical entity + Tissue, organ, system, sperm, blood or body location (arm). - An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' - Bjoern Peters - Philippe Rocca-Serra - Tina Boussard - MO + An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' + Bjoern Peters + Philippe Rocca-Serra + Tina Boussard + MO - obsolete_anatomical entity + obsolete_anatomical entity true @@ -79619,7 +97243,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA. PERSON: Maura Gasparetto PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra plasma WEB: http://en.wikipedia.org/wiki/Blood_plasma blood plasma specimen @@ -79665,7 +97289,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. PERSON: Maura Gasparetto PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/Blood_plasma blood serum specimen @@ -79693,11 +97317,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: + 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism @@ -79708,13 +97332,14 @@ This issue is outside the scope of OBI. - a single Hela cell + obsolete_immortal cell + a single Hela cell - a cell derived from a multicellular organism that has the potential to replicate indefinitely - PERSON: Bjoern Peters - GROUP: OBI Biomaterial Branch + a cell derived from a multicellular organism that has the potential to replicate indefinitely + PERSON: Bjoern Peters + GROUP: OBI Biomaterial Branch - obsolete_immortal cell + obsolete_immortal cell true @@ -79724,13 +97349,14 @@ This issue is outside the scope of OBI. - the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme + obsolete_fragment derived from protein + the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme - A material entity which is derived from a protein - PERSON: Bjoern Peters - GROUP: IEDB + A material entity which is derived from a protein + PERSON: Bjoern Peters + GROUP: IEDB - obsolete_fragment derived from protein + obsolete_fragment derived from protein true @@ -79783,7 +97409,7 @@ This issue is outside the scope of OBI. Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra PERSON: Tina Boussard PBS buffer WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline @@ -79807,12 +97433,12 @@ This issue is outside the scope of OBI. specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. - Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. - PERSON: James Malone - PERSON: Philippe Rocca-Serra + Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. + PERSON: James Malone + PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen @@ -79824,12 +97450,13 @@ This issue is outside the scope of OBI. + obsolete_cell line cell - A material entity that represents generations of a primary culture. - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch + A material entity that represents generations of a primary culture. + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch - obsolete_cell line cell + obsolete_cell line cell true @@ -79839,15 +97466,16 @@ This issue is outside the scope of OBI. + obsolete_immortal cell line culture - A cell line that is expected to be capable of indefinite propagation in an vitro culture. - PERSON:Matthew Brush - immortal cell line sample - permanent cell line - PERSON:Matthew Brush + A cell line that is expected to be capable of indefinite propagation in an vitro culture. + PERSON:Matthew Brush + immortal cell line sample + permanent cell line + PERSON:Matthew Brush - obsolete_immortal cell line culture + obsolete_immortal cell line culture true @@ -79874,7 +97502,7 @@ This issue is outside the scope of OBI. A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. PERSON: Melanie Courtot - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra xenotransplant WEB: http://en.wikipedia.org/wiki/Xenograft xenograft @@ -79904,18 +97532,18 @@ This issue is outside the scope of OBI. - cultured cell population + cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). - A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. + A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. - PERSON:Matthew Brush + PERSON:Matthew Brush cell culture sample - PERSON:Matthew Brush - The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. - cultured cell population + PERSON:Matthew Brush + The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. + cultured cell population @@ -79943,18 +97571,18 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - primary cultured cell population - Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 - cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) + primary cultured cell population + Spleen cells put directly into culture; Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934 + cells that have been isolated from some organismal source, expanded in culture, but not undergone a complete passaging (ie are still in culture, or have been lifted from culture and frozen in aliquots for future use) - A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. + A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged. 2013-6-5 MHB: This OBI class was formerly called 'primary cell culture', but label changed and definition updated following CLO alignment work. Previous definition: 'a primary cell culture is a cell culture where the cells derive from a fresh tissue source.' - PERSON:Matthew Brush - primary cell culture - primary cell culture sample - PERSON:Matthew Brush + PERSON:Matthew Brush + primary cell culture + primary cell culture sample + PERSON:Matthew Brush primary cultured cell population @@ -79976,16 +97604,17 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592. - He, Tong-Chuan, et al. Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512. - To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene. Note that common usage in the literature is often of the form a human colorectal cancer cell line, as seen above. But such references to studies in a line refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. + obsolete_cell line + A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592. + He, Tong-Chuan, et al. Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512. - To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene. Note that common usage in the literature is often of the form a human colorectal cancer cell line, as seen above. But such references to studies in a line refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'. - A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). - PERSON:Matthew Brush - cell line sample - OBI-CLO Alignment Working Group (Spring 2013) + A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). + PERSON:Matthew Brush + cell line sample + OBI-CLO Alignment Working Group (Spring 2013) - obsolete_cell line + obsolete_cell line true @@ -80000,10 +97629,10 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical. - PERSON: Susanna Sansone - PERSON:Matthew Brush + PERSON: Susanna Sansone + PERSON:Matthew Brush clonal cell culture sample - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch cultured clonal cell population @@ -80020,8 +97649,8 @@ Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39- PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application change biomaterial to material in definition PERSON: Bjoern Peters - GROUP: IEDB - 7/13/09: Need to clarify if this meets reagent role definition + GROUP: IEDB + 7/13/09: Need to clarify if this meets reagent role definition screening library @@ -80085,9 +97714,9 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ) PERSON: Helen Parkinson - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra GROUP: CEBS - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch organ section @@ -80125,13 +97754,14 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ + obsolete_polymer - A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - James Malone - Philippe Rocca-Serra - TERM: CHEBI:33839 + A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. + James Malone + Philippe Rocca-Serra + TERM: CHEBI:33839 - obsolete_polymer + obsolete_polymer true @@ -80147,13 +97777,13 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - glucose in solution - Glucose present in blood + glucose in solution + Glucose present in blood - A scattered aggregate of glucose molecules in a liquid - PERSON: Jie Zheng - glucose molecules - glucose in solution + A scattered aggregate of glucose molecules in a liquid + PERSON: Jie Zheng + glucose molecules + glucose in solution @@ -80197,20 +97827,21 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data transformation - The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. + The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors + data transformation @@ -80241,6 +97872,8 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ geometric mean calculation + + A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). Mathias Brochhausen PERSON: Mathias Brochhausen A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). @@ -80329,7 +97962,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ feature extraction objective A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. - Elisabetta Manduchi + Elisabetta Manduchi James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective @@ -80554,7 +98187,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html. Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra WEB: http://mathworld.wolfram.com/Cosine.html cosine transformation @@ -80621,7 +98254,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm. Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra PMID: 16646782 linlog transformation @@ -80662,7 +98295,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess global transformation @@ -80679,7 +98312,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess group transformation @@ -80732,7 +98365,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ Helen Parkinson James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation single @@ -80755,7 +98388,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Adjusted from MGED Ontology Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent. total intensity transformation paired @@ -80813,7 +98446,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input. Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra mean centring PERSON: Elisabetta Manduchi mean centering @@ -80836,7 +98469,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input. Elisabetta Manduchi - Philippe Rocca-Serra + Philippe Rocca-Serra median centring PERSON: Elisabetta Manduchi median centering @@ -80871,9 +98504,9 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ K-fold cross validation method - K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used - Person:Helen Parkinson - Tina Boussard + K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used + Person:Helen Parkinson + Tina Boussard K-fold cross validation method @@ -80890,11 +98523,11 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ leave one out cross validation method - The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 + The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 - is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data - 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 - Person:Helen Parkinson + is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data + 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 + Person:Helen Parkinson leave one out cross validation method @@ -80910,13 +98543,13 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - jackknifing method - simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure + jackknifing method + simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure - Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method - Helen Parkinson + Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method + Helen Parkinson jackknifing - http://en.wikipedia.org/wiki/Resampling_%28statistics%29 + http://en.wikipedia.org/wiki/Resampling_%28statistics%29 jackknifing method @@ -80933,11 +98566,11 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ boostrapping - Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. + Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient - Helen Parkinson - Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points + Helen Parkinson + Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points boostrapping @@ -80972,14 +98605,14 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ Benjamini and Hochberg false discovery rate correction method - Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate) + Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate) - A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate + A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing - Helen Parkinson + Helen Parkinson Philippe Rocca-Serra - Helen Parkinson + Helen Parkinson Benjamini and Hochberg false discovery rate correction method @@ -81047,9 +98680,9 @@ specified input and output of dt which were missing k-means clustering A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). - Elisabetta Manduchi + Elisabetta Manduchi James Malone - Philippe Rocca-Serra + Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering @@ -81119,7 +98752,7 @@ specified input and output of dt which were missing single linkage hierarchical clustering A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster. - Elisabetta Manduchi + Elisabetta Manduchi PERSON: Elisabetta Manduchi single linkage hierarchical clustering @@ -81155,14 +98788,14 @@ specified input and output of dt which were missing Benjamini and Yekutieli false discovery rate correction method - The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) + The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) - A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate + A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate 2011-03-31: [PRS]. specified input and output of dt which were missing - Helen Parkinson + Helen Parkinson Philippe Rocca-Serra - Helen Parkinson + Helen Parkinson Benjamini and Yekutieli false discovery rate correction method @@ -81192,8 +98825,8 @@ specified input and output of dt which were missing Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra - data projection + Philippe Rocca-Serra + data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot @@ -81212,7 +98845,7 @@ specified input and output of dt which were missing Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone @@ -81304,7 +98937,7 @@ specified input and output of dt which were missing A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set. Elisabetta Manduchi Helen Parkinson - Philippe Rocca-Serra + Philippe Rocca-Serra PERSON: Elisabetta Manduchi PERSON: Helen Parkinson moving average @@ -81422,7 +99055,7 @@ specified input and output of dt which were missing continuum mass spectrum A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion. - PERSON: James Malone + PERSON: James Malone PERSON: Tina Hernandez-Boussard PERSON: Tina Boussard continuum mass spectrum @@ -81464,8 +99097,8 @@ specified input and output of dt which were missing A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data. Person:Tina Hernandez-Boussard - centroid mass spectrum calculation - centroiding + centroid mass spectrum calculation + centroiding centroid mass spectrum centroid mass spectrum @@ -81495,16 +99128,16 @@ specified input and output of dt which were missing Holm-Bonferroni family-wise error rate correction method - t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179 + t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179 - a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction + a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction 2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition Also added restriction to specify the output to be a FWER adjusted p-value The 'editor preferred term' should be removed - Person:Helen Parkinson + Person:Helen Parkinson Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method + WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method Holm-Bonferroni family-wise error rate correction method @@ -81542,7 +99175,7 @@ TO BE DEALT WITH STILL BY RICHARD. JAMES Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra + Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term loess transformation @@ -81597,14 +99230,14 @@ TO BE DEALT WITH STILL BY RICHARD. JAMES family wise error rate correction method - A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. + A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive. 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt - Monnie McGee + Monnie McGee Philippe Rocca-Serra FWER correction - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 family wise error rate correction method @@ -81763,7 +99396,7 @@ allows correct classification of FWER dt An arithmetic mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. James Malone Monnie McGee - Philippe Rocca-Serra + Philippe Rocca-Serra PERSON: James Malone PERSON: Monnie McGee From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008) @@ -81780,7 +99413,7 @@ allows correct classification of FWER dt A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network. Richard Scheuermann - network topology analysis + network topology analysis PERSON: Richard Scheuermann network analysis @@ -81794,8 +99427,8 @@ allows correct classification of FWER dt sequence analysis objective A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. - James Malone - PERSON: James Malone + James Malone + PERSON: James Malone sequence analysis objective @@ -81811,12 +99444,12 @@ allows correct classification of FWER dt - longitudinal data analysis + longitudinal data analysis Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time. - PERSON: James Malone - PERSON: Tina Boussard - correlation analysis + PERSON: James Malone + PERSON: Tina Boussard + correlation analysis longitudinal data analysis longitudinal data analysis @@ -81828,13 +99461,13 @@ allows correct classification of FWER dt survival analysis objective - Kaplan meier data transformation + Kaplan meier data transformation - A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables - PERSON: James Malone - PERSON: Tina Boussard - survival analysis - http://en.wikipedia.org/wiki/Survival_analysis + A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables + PERSON: James Malone + PERSON: Tina Boussard + survival analysis + http://en.wikipedia.org/wiki/Survival_analysis survival analysis objective @@ -81852,7 +99485,7 @@ allows correct classification of FWER dt mass spectrometry analysis - A data transformation which has the objective of spectrum analysis. + A data transformation which has the objective of spectrum analysis. mass spectrometry analysis @@ -81872,7 +99505,7 @@ allows correct classification of FWER dt A spread calculation is a data transformation that has objective spread calculation. James Malone - EDITOR + EDITOR spread calculation data transformation @@ -81890,10 +99523,10 @@ allows correct classification of FWER dt Kaplan Meier - a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) - PERSON: James Malone - PERSON: Tina Boussard - http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator + a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) + PERSON: James Malone + PERSON: Tina Boussard + http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator Kaplan Meier @@ -81909,12 +99542,12 @@ allows correct classification of FWER dt - multiple testing correction method + multiple testing correction method - A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate - Monnie McGee + A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate + Monnie McGee multiple testing procedure - PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. + PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. multiple testing correction method @@ -81924,16 +99557,16 @@ allows correct classification of FWER dt - inter-rater reliability objective - A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. + inter-rater reliability objective + A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation. - a data transformation objective of determining the concordance or agreement between human judges. - Person:Alan Ruttenberg - Person:Helen Parkinson - inter-rater agreement - http://en.wikipedia.org/wiki/Inter-rater_reliability + a data transformation objective of determining the concordance or agreement between human judges. + Person:Alan Ruttenberg + Person:Helen Parkinson + inter-rater agreement + http://en.wikipedia.org/wiki/Inter-rater_reliability inter-rater reliability objective @@ -81963,11 +99596,11 @@ Examples include joint-probability of agreement, Cohen's kappa and the rela Westfall and Young family wise error rate correction - Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing + Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing 2011-03-31: [PRS]. specified input and output of dt which were missing PRS: 2011-03-31: set specified input and specified output to the data transformation - Helen Parkinson + Helen Parkinson Westfall and Young FWER correction Westfall and Young family wise error rate correction @@ -82035,11 +99668,11 @@ variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variabl - non-negative matrix factorization - Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix. + non-negative matrix factorization + Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix. - Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. - http://en.wikipedia.org/wiki/Non-negative_matrix_factorization + Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. + http://en.wikipedia.org/wiki/Non-negative_matrix_factorization non-negative matrix factorization @@ -82055,7 +99688,7 @@ variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variabl - soft independent modeling of class analogy analysis + soft independent modeling of class analogy analysis Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. Tina Hernandez-Boussard @@ -82250,10 +99883,10 @@ In this equation b0 is the regression coefficient for the intercept and the bi v partial least square discriminant analysis - PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. + PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information. James Malone PLS-DA - WEB: http://www.camo.com/rt/Resources/pls-da.html + WEB: http://www.camo.com/rt/Resources/pls-da.html partial least square discriminant analysis @@ -82378,21 +100011,21 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - data visualization - Generation of a heatmap from a microarray dataset + data visualization + Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard - data encoding as image + data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard - Possible future hierarchy might include this: + Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding @@ -82470,7 +100103,7 @@ information_encoding A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda). Monnie McGee - Philippe Rocca-Serra + Philippe Rocca-Serra ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. loess fitting @@ -82728,7 +100361,7 @@ information_encoding A data transformation in which individual input data elements and values are merged together into a output set of data elements and values. Richard Scheuermann - data pooling + data pooling editor data combination @@ -82935,12 +100568,12 @@ information_encoding - mathematical feature + mathematical feature feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review) James Malone - PERSON: James Malone + PERSON: James Malone mathematical feature @@ -82956,13 +100589,13 @@ information_encoding - log base + log base - The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1. - Elisabetta Manduchi - logarithm base - logarithmic base - WEB: http://en.wikipedia.org/wiki/Logarithm + The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1. + Elisabetta Manduchi + logarithm base + logarithmic base + WEB: http://en.wikipedia.org/wiki/Logarithm log base @@ -83064,14 +100697,14 @@ information_encoding - MA transformation - MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2. + MA transformation + MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2. - An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. - Elisabetta Manduchi - Philippe Rocca-Serra - PERSON: Elisabetta Manduchi - MA transformation + An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. + Elisabetta Manduchi + Philippe Rocca-Serra + PERSON: Elisabetta Manduchi + MA transformation @@ -83086,11 +100719,11 @@ information_encoding - exponential base + exponential base - The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). - Elisabetta Manduchi - WEB: http://en.wikipedia.org/wiki/Exponential_function + The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1). + Elisabetta Manduchi + WEB: http://en.wikipedia.org/wiki/Exponential_function exponential base @@ -83106,11 +100739,11 @@ information_encoding - polynomial degree + polynomial degree - The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi + The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi polynomial degree @@ -83126,11 +100759,11 @@ information_encoding - number of variables + number of variables - The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi + The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi number of variables @@ -83143,9 +100776,9 @@ information_encoding agglomerative hierarchical clustering An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - bottom-up hierarchical clustering + bottom-up hierarchical clustering PERSON: Elisabetta Manduchi agglomerative hierarchical clustering @@ -83159,9 +100792,9 @@ information_encoding divisive hierarchical clustering A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - top-down hierarchical clustering + top-down hierarchical clustering PERSON: Elisabetta Manduchi divisive hierarchical clustering @@ -83191,7 +100824,7 @@ information_encoding data vector reduction objective Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k. - James Malone + James Malone Richard H. Scheuermann PERSON: Richard H. Scheuermann data vector reduction objective @@ -83211,10 +100844,10 @@ information_encoding generalized family wise error rate correction method - A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. - Monnie McGee + A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. + Monnie McGee gFWER correction - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 generalized family wise error rate correction method @@ -83240,10 +100873,10 @@ information_encoding quantile number of false positives correction method - A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' - Monnie McGee + A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' + Monnie McGee QNFP - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 quantile number of false positives correction method @@ -83261,10 +100894,10 @@ information_encoding tail probability for the proportion of false positives correction method - A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. - Monnie McGee + A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. + Monnie McGee TPPFP correction method - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 tail probability for the proportion of false positives correction method @@ -83294,14 +100927,14 @@ information_encoding false discovery rate correction method - The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . + The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt - Monnie McGee + Monnie McGee Philippe Rocca-Serra FDR correction method - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate false discovery rate correction method @@ -83327,10 +100960,10 @@ allows correct classification of FDR dt proportion of expected false positives correction method - A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. - Monnie McGee + A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. + Monnie McGee PEFP correction method - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 proportion of expected false positives correction method @@ -83356,10 +100989,10 @@ allows correct classification of FDR dt quantile proportion of false positives correction method - A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). - Monnie McGee + A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). + Monnie McGee QPFP correction method - Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 + Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 quantile proportion of false positives correction method @@ -83391,11 +101024,11 @@ allows correct classification of FDR dt A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. - Elisabetta Manduchi - Helen Parkinson + Elisabetta Manduchi + Helen Parkinson James Malone - PERSON: Elisabetta Manduchi - PERSON: Helen Parkinson + PERSON: Elisabetta Manduchi + PERSON: Helen Parkinson PERSON: James Malone data normalization objective @@ -83411,8 +101044,8 @@ to create a common base for comparisons. A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself James Malone - PERSON: James Malone - PERSON: Melanie Courtot + PERSON: James Malone + PERSON: Melanie Courtot correction objective @@ -83439,7 +101072,7 @@ to create a common base for comparisons. normalization data transformation A normalization data transformation is a data transformation that has objective normalization. - James Malone + James Malone PERSON: James Malone normalization data transformation @@ -83467,7 +101100,7 @@ to create a common base for comparisons. averaging data transformation An averaging data transformation is a data transformation that has objective averaging. - James Malone + James Malone PERSON: James Malone averaging data transformation @@ -83487,7 +101120,7 @@ to create a common base for comparisons. partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. - James Malone + James Malone PERSON: James Malone partitioning data transformation @@ -83502,9 +101135,9 @@ to create a common base for comparisons. A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi + PERSON: Elisabetta Manduchi partitioning objective @@ -83517,9 +101150,9 @@ to create a common base for comparisons. background correction objective A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi + PERSON: Elisabetta Manduchi background correction objective @@ -83532,9 +101165,9 @@ to create a common base for comparisons. curve fitting objective A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints. - Elisabetta Manduchi + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi + PERSON: Elisabetta Manduchi curve fitting objective @@ -83561,9 +101194,9 @@ to create a common base for comparisons. class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. - James Malone - clustering data transformation - unsupervised classification data transformation + James Malone + clustering data transformation + unsupervised classification data transformation PERSON: James Malone class discovery data transformation @@ -83580,12 +101213,12 @@ to create a common base for comparisons. - Fisher's exact test + Fisher's exact test - Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. - James Malone - WEB:http://mathworld.wolfram.com/FishersExactTest.html - Fisher's exact test + Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests. + James Malone + WEB:http://mathworld.wolfram.com/FishersExactTest.html + Fisher's exact test @@ -83599,7 +101232,7 @@ to create a common base for comparisons. A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. James Malone - PERSON: James Malone + PERSON: James Malone center calculation objective @@ -83613,11 +101246,11 @@ to create a common base for comparisons. A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone - clustering objective + clustering objective discriminant analysis objective unsupervised classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone + PERSON: Elisabetta Manduchi + PERSON: James Malone class discovery objective @@ -83632,10 +101265,10 @@ to create a common base for comparisons. A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone - classification objective + classification objective supervised classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone + PERSON: Elisabetta Manduchi + PERSON: James Malone class prediction objective @@ -83646,12 +101279,12 @@ class labels for these objects. The resulting predictor can be used to attach cl spread calculation objective - Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean + Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean - is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set + is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set Awaiting English definition from Monnie McGee James Malone - Person:Helen Parkinson + Person:Helen Parkinson spread calculation objective @@ -83678,7 +101311,7 @@ class labels for these objects. The resulting predictor can be used to attach cl center calculation data transformation A center calculation data transformation is a data transformation that has objective of center calculation. - James Malone + James Malone PERSON: James Malone center calculation data transformation @@ -83718,12 +101351,12 @@ class labels for these objects. The resulting predictor can be used to attach cl scaling objective - Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 + Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 - is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum + is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum Awaiting English definition from Monnie McGee James Malone - Person:Helen Parkinson + Person:Helen Parkinson scaling objective @@ -83782,11 +101415,11 @@ class labels for these objects. The resulting predictor can be used to attach cl error correction objective - Application of a multiple testing correction method + Application of a multiple testing correction method An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. James Malone, Helen Parkinson - PERSON: James Malone + PERSON: James Malone error correction objective @@ -83806,7 +101439,7 @@ class labels for these objects. The resulting predictor can be used to attach cl A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns. James Malone - EDITOR + EDITOR sequence analysis data transformation @@ -83821,7 +101454,7 @@ class labels for these objects. The resulting predictor can be used to attach cl A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective - WEB: http://en.wikipedia.org/wiki/Cross_validation + WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective @@ -83831,13 +101464,13 @@ class labels for these objects. The resulting predictor can be used to attach cl - merging objective + merging objective merging of columns from two different data sets A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. James Malone combining objective - PERSON: Data Transformation Branch + PERSON: Data Transformation Branch merging objective @@ -83869,11 +101502,11 @@ class labels for these objects. The resulting predictor can be used to attach cl - clustered data visualization + clustered data visualization - A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. - James Malone - clustered data visualization + A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. + James Malone + clustered data visualization @@ -83894,11 +101527,11 @@ class labels for these objects. The resulting predictor can be used to attach cl - gene list visualization + gene list visualization - Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type. - James Malone - gene list visualization + Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type. + James Malone + gene list visualization @@ -83926,11 +101559,11 @@ class labels for these objects. The resulting predictor can be used to attach cl - classified data visualization + classified data visualization - A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type. - James Malone - classified data visualization + A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type. + James Malone + classified data visualization @@ -83958,12 +101591,12 @@ class labels for these objects. The resulting predictor can be used to attach cl - background corrected data visualization + background corrected data visualization - A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type. - James Malone - Monnie McGee - background corrected data visualization + A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type. + James Malone + Monnie McGee + background corrected data visualization @@ -83978,12 +101611,12 @@ class labels for these objects. The resulting predictor can be used to attach cl - survival analysis data transformation + survival analysis data transformation - A data transformation which has the objective of performing survival analysis. - James Malone - PERSON: James Malone - survival analysis data transformation + A data transformation which has the objective of performing survival analysis. + James Malone + PERSON: James Malone + survival analysis data transformation @@ -83998,15 +101631,15 @@ class labels for these objects. The resulting predictor can be used to attach cl - proportional hazards model estimation + proportional hazards model estimation - Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. - PERSON: James Malone - PERSON: Tina Boussard - Cox model - Cox proportional hazards model - WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model - proportional hazards model estimation + Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. + PERSON: James Malone + PERSON: Tina Boussard + Cox model + Cox proportional hazards model + WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model + proportional hazards model estimation @@ -84015,11 +101648,11 @@ class labels for these objects. The resulting predictor can be used to attach cl - correlation study objective + correlation study objective - A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. - PERSON: Tina Boussard - correlation study objective + A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables. + PERSON: Tina Boussard + correlation study objective @@ -84028,13 +101661,13 @@ class labels for these objects. The resulting predictor can be used to attach cl - spectrum analysis objective - Calculation of characteristic path length in mass spectrometry + spectrum analysis objective + Calculation of characteristic path length in mass spectrometry - is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. - PERSON: Tina Boussard - Person:Helen Parkinson - spectrum analysis objective + is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. + PERSON: Tina Boussard + Person:Helen Parkinson + spectrum analysis objective @@ -84049,14 +101682,14 @@ class labels for these objects. The resulting predictor can be used to attach cl - tandem mass spectrometry - A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS. + tandem mass spectrometry + A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS. - Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). - PERSON: James Malone - PERSON: Tina Boussard - PERSON: Tina Boussard - tandem mass spectrometry + Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). + PERSON: James Malone + PERSON: Tina Boussard + PERSON: Tina Boussard + tandem mass spectrometry @@ -84071,15 +101704,15 @@ class labels for these objects. The resulting predictor can be used to attach cl - gas chromatography mass spectrometry + gas chromatography mass spectrometry - Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and + Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determinations of compounds. - PERSON: James Malone - PERSON: Tina Boussard - PERSON: Tina Boussard - gas chromatography mass spectrometry + PERSON: James Malone + PERSON: Tina Boussard + PERSON: Tina Boussard + gas chromatography mass spectrometry @@ -84094,12 +101727,12 @@ determinations of compounds. - chi square test + chi square test - The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. - PERSON: James Malone - PERSON: Tina Boussard - chi square test + The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough. + PERSON: James Malone + PERSON: Tina Boussard + chi square test @@ -84108,11 +101741,11 @@ determinations of compounds. - ANOVA + ANOVA - ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal. - James Malone - ANOVA + ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal. + James Malone + ANOVA @@ -84121,14 +101754,14 @@ determinations of compounds. - sequential design - PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. + sequential design + PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. - Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does - Philippe Rocca-Serra - MUSC - Provenance: OCI - sequential design + Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does + Philippe Rocca-Serra + MUSC + Provenance: OCI + sequential design @@ -84137,13 +101770,13 @@ determinations of compounds. - observation design - PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. + observation design + PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. - observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. - Philippe Rocca-Serra - OBI branch derived - observation design + observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. + Philippe Rocca-Serra + OBI branch derived + observation design @@ -84152,16 +101785,17 @@ determinations of compounds. - PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings] - - a collection is a bfo:aggregate object, that is a set of material object of the same kind - PERSON: Susanna Sansone - ensemble - group - set - PERSON: Philippe Rocca-Serra + obsolete_collection (of entities of organismal origin) + PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings] + + a collection is a bfo:aggregate object, that is a set of material object of the same kind + PERSON: Susanna Sansone + ensemble + group + set + PERSON: Philippe Rocca-Serra - obsolete_collection (of entities of organismal origin) + obsolete_collection (of entities of organismal origin) true @@ -84195,8 +101829,8 @@ determinations of compounds. A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish - PERSON: Jennifer Fostel - GROUP: CEBS + PERSON: Jennifer Fostel + GROUP: CEBS pool of specimens @@ -84244,10 +101878,10 @@ determinations of compounds. PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution. A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute. - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra liquid chemical solution - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch chemical solution @@ -84257,14 +101891,14 @@ determinations of compounds. - buffer role - A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution + buffer role + A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3-) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution - a role which inheres in some molecular entity realized during the process of buffering - Person:Helen Parkinson - Person:Philippe Rocca-Serra - buffer - OBI + a role which inheres in some molecular entity realized during the process of buffering + Person:Helen Parkinson + Person:Philippe Rocca-Serra + buffer + OBI buffer role @@ -84286,12 +101920,12 @@ determinations of compounds. - solvent role + solvent role PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors. solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation - Philippe Rocca-Serra - adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) + Philippe Rocca-Serra + adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) solvent role @@ -84313,12 +101947,12 @@ determinations of compounds. - solute role + solute role PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure. solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution - Philippe Rocca-Serra - adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) + Philippe Rocca-Serra + adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) solute role @@ -84450,14 +102084,15 @@ determinations of compounds. - PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. + comet assay + PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. - An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis - Philippe Rocca-Serra - SCGE assay - single cell gel electrophoresis assay - PMID:7686265 - comet assay + An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis + Philippe Rocca-Serra + SCGE assay + single cell gel electrophoresis assay + PMID:7686265 + comet assay @@ -84497,13 +102132,14 @@ determinations of compounds. - PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? + PCR-SSCP assay + PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? - An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions - Philippe Rocca-Serra - polymerase chain reaction-single strand conformation polymorphism assay - PMID:18219595 - PCR-SSCP assay + An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions + Philippe Rocca-Serra + polymerase chain reaction-single strand conformation polymorphism assay + PMID:18219595 + PCR-SSCP assay @@ -84512,13 +102148,14 @@ determinations of compounds. - PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93. + obsolete_liver + PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93. - liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial Branch + liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial Branch - obsolete_liver + obsolete_liver true @@ -84528,13 +102165,14 @@ determinations of compounds. - PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4. + obsolete_adipose tissue + PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4. - adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates. - PERSON: Philippe Rocca-Serra - GROUP: OBI Biomaterial derived + adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates. + PERSON: Philippe Rocca-Serra + GROUP: OBI Biomaterial derived - obsolete_adipose tissue + obsolete_adipose tissue true @@ -84554,11 +102192,11 @@ determinations of compounds. - denatured polymer + denatured polymer Is a polymer which has lost secondary or tertiary structure - PERSON: Alan Ruttenberg - http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 + PERSON: Alan Ruttenberg + http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 denatured polymer @@ -84578,12 +102216,12 @@ determinations of compounds. - decapitated organism + decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 decapitated organism is an organism which has had it's head removed - Philippe Rocca-Serra + Philippe Rocca-Serra OBI Biomaterial decapitated organism @@ -84600,12 +102238,12 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - validated information - PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." + validated information + PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means. - Person:Philippe Rocca-Serra - OBI + Person:Philippe Rocca-Serra + OBI validated information @@ -84621,15 +102259,15 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - curated information - PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. + curated information + PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. - A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts. - 2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions. - 2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference - Person:Bjoern Peters - Person:Philippe Rocca-Serra - OBI + An information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts. + 2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions. + 2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference + Person:Bjoern Peters + Person:Philippe Rocca-Serra + OBI curated information @@ -84645,12 +102283,12 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - randomized group participant role - A person enrolled in a randomized clinical trial bears a randomized group participant role + randomized group participant role + A person enrolled in a randomized clinical trial bears a randomized group participant role - a role that borne by an organism and realized by some group randomization process - Person:Helen Parkinson - Philippe Rocca-Serra + a role that borne by an organism and realized by some group randomization process + Person:Helen Parkinson + Philippe Rocca-Serra randomized group participant role @@ -84670,12 +102308,12 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - methylated polymer + methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 A methylated polymer which has artificially acquired one or more methyl groups - Philippe Rocca-Serra + Philippe Rocca-Serra OBI Biomaterial methylated polymer @@ -84696,12 +102334,12 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 - genetically modified organism + genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 an organism that is the output of a genetic transformation process - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra OBI Biomaterial genetically modified organism @@ -84718,11 +102356,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - predicted data item + predicted data item A data item that was generated on the basis of a calculation or logical reasoning - BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. - Philippe Rocca-Serra; Bjoern Peters + BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. + Philippe Rocca-Serra; Bjoern Peters predicted data item @@ -84738,11 +102376,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - mean-centered data + mean-centered data - a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value - Person:Helen Parkinson - Person:Philippe Rocca-Serra + a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value + Person:Helen Parkinson + Person:Philippe Rocca-Serra mean-centered data @@ -84758,12 +102396,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - edited document - The OBI manuscript is (much) edited imformation + edited document + The OBI manuscript is (much) edited imformation - A document which is the output of a document editing process - Person:Bjoern Peters - Philippe Rocca-Serra + A document which is the output of a document editing process + Person:Bjoern Peters + Philippe Rocca-Serra edited document @@ -84789,12 +102427,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - dissolved material entity - Salt molecules that have been mixed into water + dissolved material entity + Salt molecules that have been mixed into water - A material entity that has been going through a process of being put into solution - Person:Bjoern Peters - Philippe Rocca-Serra + A material entity that has been going through a process of being put into solution + Person:Bjoern Peters + Philippe Rocca-Serra dissolved material entity @@ -84810,14 +102448,14 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - extraction - nucleic acid extraction using phenol chloroform + extraction + nucleic acid extraction using phenol chloroform - A material separation in which a desired component of an input material is separated from the remainder + A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. - Person:Bjoern Peters - Philippe Rocca-Serra + Person:Bjoern Peters + Philippe Rocca-Serra extraction @@ -84839,12 +102477,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - filtration + filtration PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4. filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device - Philippe Rocca-Serra - OBI-Branch: adapted from wikipedia and wordnet + Philippe Rocca-Serra + OBI-Branch: adapted from wikipedia and wordnet filtration @@ -84866,12 +102504,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - centrifugation + centrifugation PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12. centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation - Philippe Rocca-Serra - adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm + Philippe Rocca-Serra + adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm centrifugation @@ -84887,12 +102525,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - staining + staining PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8. Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound. - Philippe Rocca-Serra - adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining + Philippe Rocca-Serra + adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining staining @@ -84920,12 +102558,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - washing + washing PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4. washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow. - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch washing @@ -84953,12 +102591,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - irradiation + irradiation PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370. irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves - Philippe Rocca-Serra - adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) + Philippe Rocca-Serra + adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) irradiation @@ -84986,13 +102624,13 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - polymerization + polymerization PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3. polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight PRS:22102008: need to import catalyst from CHEBI 35223 - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch polymerization @@ -85002,12 +102640,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - trypsination + trypsination The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483 trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity - Philippe Rocca-Serra - OBI PA + Philippe Rocca-Serra + OBI PA trypsination @@ -85039,12 +102677,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - enzymatic ligation + enzymatic ligation PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch enzymatic ligation @@ -85066,12 +102704,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - storage + storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch storage @@ -85094,13 +102732,13 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - cell lysis + cell lysis PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41. cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock. - BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process. - Philippe Rocca-Serra - adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] + BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process. + Philippe Rocca-Serra + adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] cell lysis @@ -85116,12 +102754,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - electrocution + electrocution PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376. electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process. - Philippe Rocca-Serra - OBI branch + Philippe Rocca-Serra + OBI branch electrocution @@ -85131,13 +102769,13 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - cervical dislocation + cervical dislocation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3 cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax) - Philippe Rocca-Serra - OBI branch + Philippe Rocca-Serra + OBI branch cervical dislocation @@ -85147,12 +102785,12 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - asphyxiation + asphyxiation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570- asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms. - Philippe Rocca-Serra - OBI branch + Philippe Rocca-Serra + OBI branch asphyxiation @@ -85168,14 +102806,14 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - intentional overdosing + intentional overdosing In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment. J Neurooncol. 1994;22(3):209-20. PMID: 7760097 intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death - Philippe Rocca-Serra + Philippe Rocca-Serra lethal injection - OBI Biomaterial + OBI Biomaterial intentional overdosing @@ -85185,12 +102823,12 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - decapitation + decapitation PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570- decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..) - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch decapitation @@ -85200,12 +102838,12 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - group randomization + group randomization PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6. A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up. - Philippe Rocca-Serra - adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] + Philippe Rocca-Serra + adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization] group randomization @@ -85215,13 +102853,14 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63. + obsolete_activation + PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63. - a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!) - Philippe Rocca-Serra - OBI-Branch + a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!) + Philippe Rocca-Serra + OBI-Branch - obsolete_activation + obsolete_activation true @@ -85237,12 +102876,12 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - immobilization + immobilization PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23. immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum. - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch immobilization @@ -85268,13 +102907,13 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - nucleic acid hybridization + nucleic acid hybridization PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27. a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity. - Philippe Rocca-Serra - adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] - hybridization assay + Philippe Rocca-Serra + adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] + hybridization assay nucleic acid hybridization @@ -85318,12 +102957,12 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - elution + elution PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13. the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions) - Philippe Rocca-Serra - wordnet.princeton.edu/perl/webwn + Philippe Rocca-Serra + wordnet.princeton.edu/perl/webwn elution @@ -85343,8 +102982,8 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81 a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. - Philippe Rocca-Serra - OBI-Branch + Philippe Rocca-Serra + OBI-Branch DNA Subtraction @@ -85366,13 +103005,13 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - document editing + document editing Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292 is a planned process with specified input original document and specified output edited document - Philippe Rocca-Serra and OBI consortium - adapted from wikipedia + Philippe Rocca-Serra and OBI consortium + adapted from wikipedia document editing @@ -85394,12 +103033,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - prediction + prediction Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190 a process by which an event or an entity is described before it actually happens or is being discovered and identified. - Philippe Rocca-Serra - OBI + Philippe Rocca-Serra + OBI prediction @@ -85409,12 +103048,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - validation + validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results - Philippe Rocca-Serra - adapted from wordnet (wkipedia) + Philippe Rocca-Serra + adapted from wordnet (wkipedia) validation @@ -85436,13 +103075,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - electroporation + electroporation PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13. a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA - Philippe Rocca-Serra - electropermeabilization - WEB:http://en.wikipedia.org/wiki/Electroporation + Philippe Rocca-Serra + electropermeabilization + WEB:http://en.wikipedia.org/wiki/Electroporation electroporation @@ -85452,12 +103091,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - digital curation + digital curation PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44. Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally. - Philippe Rocca-Serra - wikipedia + Philippe Rocca-Serra + wikipedia digital curation @@ -85467,12 +103106,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - A10-Analyzer + A10-Analyzer - A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. - John Quinn - http://www.apogeeflow.com/flow_cytometry_products.htm - A10-Analyzer + A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells. + John Quinn + http://www.apogeeflow.com/flow_cytometry_products.htm + A10-Analyzer @@ -85481,12 +103120,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - A40-MiniFCM + A40-MiniFCM - A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. - John Quinn - http://www.apogeeflow.com/flow_cytometry_products.htm - A40-MiniFCM + A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. + John Quinn + http://www.apogeeflow.com/flow_cytometry_products.htm + A40-MiniFCM @@ -85501,16 +103140,16 @@ Manual editing of automatically recorded data in an anesthesia information manag - analog-to-digital converter - The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. + analog-to-digital converter + The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. - An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. - John Quinn - Melanie Courtot - A-D - A2D - http://en.wiktionary.org/wiki/Analog-to-Digital_Converter - analog-to-digital converter + An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal. + John Quinn + Melanie Courtot + A-D + A2D + http://en.wiktionary.org/wiki/Analog-to-Digital_Converter + analog-to-digital converter @@ -85549,13 +103188,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - flow cytometer analyzer - FACS Calibur, Luminex 100 + flow cytometer analyzer + FACS Calibur, Luminex 100 - An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis. - John Quinn - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - flow cytometer analyzer + An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis. + John Quinn + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + flow cytometer analyzer @@ -85564,13 +103203,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - arc lamp - The Jablochkoff Candle + arc lamp + The Jablochkoff Candle - Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point. - John Quinn - http://en.wikipedia.org/wiki/Arc_lamp - arc lamp + Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point. + John Quinn + http://en.wikipedia.org/wiki/Arc_lamp + arc lamp @@ -85579,14 +103218,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - argon ion laser - argon ion laser in a cytometer + argon ion laser + argon ion laser in a cytometer - An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes. - Daniel Schober - John Quinn - http://en.wikipedia.org/wiki/Laser#Gas_lasers - argon ion laser + An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes. + Daniel Schober + John Quinn + http://en.wikipedia.org/wiki/Laser#Gas_lasers + argon ion laser @@ -85595,13 +103234,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - avalanche photodiode - C30644E - InGaAs Avalanche Photodiode + avalanche photodiode + C30644E - InGaAs Avalanche Photodiode - An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - avalanche photodiode + An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + avalanche photodiode @@ -85610,12 +103249,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Bactiflow + Bactiflow - A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes. - John Quinn - http://www.chemunex.com/products/chemframe.htm - Bactiflow + A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes. + John Quinn + http://www.chemunex.com/products/chemframe.htm + Bactiflow @@ -85624,13 +103263,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - band pass filter - 530/30 BP filter, 585/42 BP filter + band pass filter + 530/30 BP filter, 585/42 BP filter - A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others. - Person:John Quinn - http://en.wikipedia.org/wiki/Band_pass_filter - band pass filter + A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others. + Person:John Quinn + http://en.wikipedia.org/wiki/Band_pass_filter + band pass filter @@ -85639,13 +103278,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - BioSorter1000 - BioSorter 1000 at TSRI Flow Cytometry Core Facility + BioSorter1000 + BioSorter 1000 at TSRI Flow Cytometry Core Facility - A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter. - John Quinn - http://www.unionbio.com/products/BioSorter.html - BioSorter1000 + A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter. + John Quinn + http://www.unionbio.com/products/BioSorter.html + BioSorter1000 @@ -85654,13 +103293,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - BioSorter2000 - BioSorter 2000 at TSRI Flow Cytometry Core Facility + BioSorter2000 + BioSorter 2000 at TSRI Flow Cytometry Core Facility - A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter. - John Quinn - http://www.unionbio.com/products/BioSorter.html - BioSorter2000 + A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter. + John Quinn + http://www.unionbio.com/products/BioSorter.html + BioSorter2000 @@ -85669,13 +103308,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - BioSorter250 - BioSorter 250 at TSRI Flow Cytometry Core Facility + BioSorter250 + BioSorter 250 at TSRI Flow Cytometry Core Facility - A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter. - John Quinn - http://www.unionbio.com/products/BioSorter.html - BioSorter250 + A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter. + John Quinn + http://www.unionbio.com/products/BioSorter.html + BioSorter250 @@ -85684,13 +103323,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - BioSorter500 - BioSorter 500 at TSRI Flow Cytometry Core Facility + BioSorter500 + BioSorter 500 at TSRI Flow Cytometry Core Facility - A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length. - John Quinn - http://www.unionbio.com/products/BioSorter.html - BioSorter500 + A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length. + John Quinn + http://www.unionbio.com/products/BioSorter.html + BioSorter500 @@ -85699,12 +103338,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Cell Lab Quanta SC + Cell Lab Quanta SC - A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells. - John Quinn - http://www.beckmancoulter.com/cell-lab - Cell Lab Quanta SC + A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells. + John Quinn + http://www.beckmancoulter.com/cell-lab + Cell Lab Quanta SC @@ -85725,13 +103364,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - charge plate - LSR2 charge plate + charge plate + LSR2 charge plate - Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - charge plate + Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + charge plate @@ -85740,13 +103379,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - cell sorter collection tube - LSR2 collection tube + cell sorter collection tube + LSR2 collection tube - Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - cell sorter collection tube + Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + cell sorter collection tube @@ -85755,12 +103394,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Cyan + Cyan - A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells. - John Quinn - http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm - Cyan + A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells. + John Quinn + http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm + Cyan @@ -85769,12 +103408,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CYFlow ML + CYFlow ML - A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting. - John Quinn - http://www.partec.de/products/cyflow-ml.html - CYFlow ML + A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting. + John Quinn + http://www.partec.de/products/cyflow-ml.html + CYFlow ML @@ -85783,12 +103422,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CyFlow SL + CyFlow SL - a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels. - John Quinn - http://www.partec.de/products/cyflow.html - CyFlow SL + a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels. + John Quinn + http://www.partec.de/products/cyflow.html + CyFlow SL @@ -85797,12 +103436,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CyFlow SL3 + CyFlow SL3 - A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement. - John Quinn - http://www.partec.de/products/cyflowsl3.html - CyFlow SL3 + A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement. + John Quinn + http://www.partec.de/products/cyflowsl3.html + CyFlow SL3 @@ -85811,13 +103450,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - CyFlow Space - CyFlow Space at TSRI Flow Cytometry Core Facility + CyFlow Space + CyFlow Space at TSRI Flow Cytometry Core Facility - A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research. - John Quinn - http://www.partec.de/products/cyflowspace.html - CyFlow Space + A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research. + John Quinn + http://www.partec.de/products/cyflowspace.html + CyFlow Space @@ -85832,13 +103471,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - CytoBuoy - CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations + CytoBuoy + CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations - A flow cytometer analyser which is manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. - John Quinn, Melanie Courtot - http://www.cytobuoy.com/ - CytoBuoy flow cytometer analyzer + A flow cytometer analyser which is manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. + John Quinn, Melanie Courtot + http://www.cytobuoy.com/ + CytoBuoy flow cytometer analyzer @@ -85847,12 +103486,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CytoSence + CytoSence - A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites. - John Quinn - http://www.cytobuoy.com/ - CytoSence + A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites. + John Quinn + http://www.cytobuoy.com/ + CytoSence @@ -85861,12 +103500,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - CytoSub + CytoSub - A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle. - John Quinn - http://www.cytobuoy.com/ - CytoSub + A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle. + John Quinn + http://www.cytobuoy.com/ + CytoSub @@ -85875,13 +103514,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - dichroic filter - Cy3 Dichroic Filter + dichroic filter + Cy3 Dichroic Filter - A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. - John Quinn - http://en.wikipedia.org/wiki/Dichroic_filter - dichroic filter + A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. + John Quinn + http://en.wikipedia.org/wiki/Dichroic_filter + dichroic filter @@ -85890,13 +103529,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - dichroic mirror - ViewLux Alexa 594 dichroic mirror + dichroic mirror + ViewLux Alexa 594 dichroic mirror - A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. - John Quinn - http://en.wikipedia.org/wiki/Dichroic_mirror - dichroic mirror + A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light. + John Quinn + http://en.wikipedia.org/wiki/Dichroic_mirror + dichroic mirror @@ -85911,13 +103550,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - differential pressure gauge - LSR2 differential pressure gauge + differential pressure gauge + LSR2 differential pressure gauge - Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - differential pressure gauge + Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + differential pressure gauge @@ -85926,13 +103565,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - diode laser - FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc. + diode laser + FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc. - A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer. - Daniel Schober - John Quinn - diode laser + A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer. + Daniel Schober + John Quinn + diode laser @@ -85941,14 +103580,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - dye laser - Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. + dye laser + Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. - A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification. - Daniel Schober - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - dye laser + A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification. + Daniel Schober + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + dye laser @@ -85957,13 +103596,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACS Calibur - FACS Calibur at TFL, BCCRC, Vancouver + FACS Calibur + FACS Calibur at TFL, BCCRC, Vancouver - The FACS Calibur is one of the most popular cytometers in use for research. - John Quinn - http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11 - FACS Calibur + The FACS Calibur is one of the most popular cytometers in use for research. + John Quinn + http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11 + FACS Calibur @@ -85972,12 +103611,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACS Canto + FACS Canto - A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications. - John Quinn - http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf - FACS Canto + A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications. + John Quinn + http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf + FACS Canto @@ -85986,12 +103625,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACS Canto2 + FACS Canto2 - A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications. - John Quinn - http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01 - FACS Canto2 + A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications. + John Quinn + http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01 + FACS Canto2 @@ -86000,12 +103639,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACS Scan + FACS Scan - A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications. - John Quinn - http://www.brc.ubc.ca/brc/facs.html - FACS Scan + A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications. + John Quinn + http://www.brc.ubc.ca/brc/facs.html + FACS Scan @@ -86014,13 +103653,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACSAria - FACSAria at TSRI Flow Cytometry Core Facility + FACSAria + FACSAria at TSRI Flow Cytometry Core Facility - A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters. - John Quinn - http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf - FACSAria + A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters. + John Quinn + http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf + FACSAria @@ -86029,13 +103668,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - FACSvantage - FACSvantage at TSRI Flow Cytometry Core Facility + FACSvantage + FACSvantage at TSRI Flow Cytometry Core Facility - The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells. - John Quinn - http://www.bdbiosciences.com/features/products/display_product.php?keyID=42 - FACSvantage + The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells. + John Quinn + http://www.bdbiosciences.com/features/products/display_product.php?keyID=42 + FACSvantage @@ -86044,12 +103683,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - FC 500 + FC 500 - A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications. - John Quinn - http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp - FC 500 + A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications. + John Quinn + http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp + FC 500 @@ -86064,14 +103703,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - flow cell - Biofilm Flow Cell + flow cell + Biofilm Flow Cell - Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. - Person:John Quinn - flow_cell - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - flow cell + Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. + Person:John Quinn + flow_cell + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + flow cell @@ -86116,13 +103755,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - flow cytometer - FACS Calibur + flow cytometer + FACS Calibur - A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. - John Quinn - http://en.wikipedia.org/wiki/Flow_cytometer - flow cytometer + A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium. + John Quinn + http://en.wikipedia.org/wiki/Flow_cytometer + flow cytometer @@ -86143,13 +103782,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - fluid pressure regulator - LSR2 fluid pressure regulator + fluid pressure regulator + LSR2 fluid pressure regulator - Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. - Person: John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - fluid pressure regulator + Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank. + Person: John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + fluid pressure regulator @@ -86158,14 +103797,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - gas laser - helium-neon gas laser used to erradiate cells in a flow cytometer. + gas laser + helium-neon gas laser used to erradiate cells in a flow cytometer. - A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas. - Daniel Schober - John Quinn - http://en.wikipedia.org/wiki/Gas_laser - gas laser + A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas. + Daniel Schober + John Quinn + http://en.wikipedia.org/wiki/Gas_laser + gas laser @@ -86174,12 +103813,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Guava EasyCyte Mini + Guava EasyCyte Mini - A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement. - John Quinn - http://www.guavatechnologies.com/main/products/easyCyteMini.cfm - Guava EasyCyte Mini + A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement. + John Quinn + http://www.guavatechnologies.com/main/products/easyCyteMini.cfm + Guava EasyCyte Mini @@ -86188,12 +103827,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Guava EasyCyte Plus + Guava EasyCyte Plus - A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement. - John Quinn - http://www.guavatechnologies.com/main/products/easycyte-new.cfm - Guava EasyCyte Plus + A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement. + John Quinn + http://www.guavatechnologies.com/main/products/easycyte-new.cfm + Guava EasyCyte Plus @@ -86202,13 +103841,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - Guava Personal Cell Analysis + Guava Personal Cell Analysis - A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement. - John Quinn - Guava_PCA - http://www.guavatechnologies.com/main/products/PCA-new.cfm - Guava Personal Cell Analysis + A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement. + John Quinn + Guava_PCA + http://www.guavatechnologies.com/main/products/PCA-new.cfm + Guava Personal Cell Analysis @@ -86217,13 +103856,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - Guava Personal Cell Analysis-96 + Guava Personal Cell Analysis-96 - The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. - John Quinn - Guava_PCA-96 - http://www.guavatechnologies.com/main/products/PCA-96new.cfm - Guava Personal Cell Analysis-96 + The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement. + John Quinn + Guava_PCA-96 + http://www.guavatechnologies.com/main/products/PCA-96new.cfm + Guava Personal Cell Analysis-96 @@ -86232,13 +103871,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - helium cadmium ion laser - KIMMON HeCd 325nm laser + helium cadmium ion laser + KIMMON HeCd 325nm laser - A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer. - John Quinn - http://en.wikipedia.org/wiki/Laser#Gas_lasers - helium cadmium ion laser + A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer. + John Quinn + http://en.wikipedia.org/wiki/Laser#Gas_lasers + helium cadmium ion laser @@ -86247,14 +103886,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - helium neon ion laser - A helium neon laser can by used to irradiate cells in a flow cytometer. + helium neon ion laser + A helium neon laser can by used to irradiate cells in a flow cytometer. - A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm. - Daniel Schober - John Quinn - http://en.wikipedia.org/wiki/Laser#Gas_lasers - helium neon ion laser + A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm. + Daniel Schober + John Quinn + http://en.wikipedia.org/wiki/Laser#Gas_lasers + helium neon ion laser @@ -86275,14 +103914,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - Amnis ImageStream + Amnis ImageStream - The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow. It has both components, an Image cytometer and a flow cytometer. - It has both components, an Image cytometer and a flow cytometer. - John Quinn - Melanie Courtot - http://www.amnis.com/ - Amnis ImageStream + The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow. It has both components, an Image cytometer and a flow cytometer. + It has both components, an Image cytometer and a flow cytometer. + John Quinn + Melanie Courtot + http://www.amnis.com/ + Amnis ImageStream @@ -86291,12 +103930,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - inFlux Analyzer + inFlux Analyzer - The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells. - John Quinn - http://www.cytopeia.com/analyzer.htm - inFlux Analyzer + The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells. + John Quinn + http://www.cytopeia.com/analyzer.htm + inFlux Analyzer @@ -86305,13 +103944,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - Influx Cell Sorter - Influx Cell Sorter at TSRI Flow Cytometry Core Facility + Influx Cell Sorter + Influx Cell Sorter at TSRI Flow Cytometry Core Facility - A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells. - John Quinn - http://www.cytopeia.com/sorter.htm - Influx Cell Sorter + A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells. + John Quinn + http://www.cytopeia.com/sorter.htm + Influx Cell Sorter @@ -86335,14 +103974,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - ion laser - 2 Watt Lexel 88 Argon Ion laser + ion laser + 2 Watt Lexel 88 Argon Ion laser - An ion laser is a gas laser which uses an ionized gas as its lasing medium. - Daniel Schober - John Quinn - http://en.wikipedia.org/wiki/Ion_laser - ion laser + An ion laser is a gas laser which uses an ionized gas as its lasing medium. + Daniel Schober + John Quinn + http://en.wikipedia.org/wiki/Ion_laser + ion laser @@ -86366,13 +104005,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - krypton ion laser - Lexel 95L krypton laser + krypton ion laser + Lexel 95L krypton laser - A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however. - Daniel Schober - John Quinn - krypton ion laser + A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however. + Daniel Schober + John Quinn + krypton ion laser @@ -86381,14 +104020,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - LactoScope C4 - LactoScope C4 Automatic Economical + LactoScope C4 + LactoScope C4 Automatic Economical - A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy. - Josef Spidlen - Melanie Courtot - http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm - LactoScope C4 + A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy. + Josef Spidlen + Melanie Courtot + http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm + LactoScope C4 @@ -86397,15 +104036,15 @@ Manual editing of automatically recorded data in an anesthesia information manag - laser - A laser is the most common way to irradiate a cell in a flow cytometer. + laser + A laser is the most common way to irradiate a cell in a flow cytometer. - A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. - Daniel Schober - light amplification by the stimulated emission of radiation - John Quinn - http://en.wikipedia.org/wiki/Laser - laser + A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer. + Daniel Schober + light amplification by the stimulated emission of radiation + John Quinn + http://en.wikipedia.org/wiki/Laser + laser @@ -86420,14 +104059,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - light source + light source - A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. - Elizabeth M. Goralczyk - John Quinn - Olga Tchuvatkina - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - light source + A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser. + Elizabeth M. Goralczyk + John Quinn + Olga Tchuvatkina + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + light source @@ -86436,13 +104075,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - logarithmic voltage amplifier - HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH + logarithmic voltage amplifier + HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH - A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - logarithmic voltage amplifier + A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + logarithmic voltage amplifier @@ -86451,13 +104090,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - long pass filter - 750 LP filter + long pass filter + 750 LP filter - A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm. - John Quinn - http://en.wikipedia.org/wiki/high-pass_filter - long pass filter + A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm. + John Quinn + http://en.wikipedia.org/wiki/high-pass_filter + long pass filter @@ -86466,13 +104105,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - LSR2 - LSR2 at TSRI Flow Cytometry Core Facility + LSR2 + LSR2 at TSRI Flow Cytometry Core Facility - A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use. - John Quinn - http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf - LSR2 + A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use. + John Quinn + http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf + LSR2 @@ -86481,12 +104120,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Luminex 100 + Luminex 100 - The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette. - John Quinn - http://www.luminexcorp.com/products/luminex_100IS.html - Luminex 100 + The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette. + John Quinn + http://www.luminexcorp.com/products/luminex_100IS.html + Luminex 100 @@ -86495,12 +104134,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Luminex 200 + Luminex 200 - A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation - John Quinn - http://www.luminexcorp.com/support/faqs.html - Luminex 200 + A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation + John Quinn + http://www.luminexcorp.com/support/faqs.html + Luminex 200 @@ -86509,12 +104148,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - MACS Quant + MACS Quant - A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications. - John Quinn - http://www.miltenyi.com - MACS Quant + A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications. + John Quinn + http://www.miltenyi.com + MACS Quant @@ -86523,13 +104162,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - metal vapor laser - Gold vapor laser, Helium-cadmium metal-vapor laser + metal vapor laser + Gold vapor laser, Helium-cadmium metal-vapor laser - A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - metal vapor laser + A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + metal vapor laser @@ -86538,13 +104177,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - mixed argon-krypton gas laser - argon-krypton laser in a cytometer + mixed argon-krypton gas laser + argon-krypton laser in a cytometer - A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer. - John Quinn - http://www.eio.com/repairfaq/sam/laserarg.htm - mixed argon-krypton gas laser + A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer. + John Quinn + http://www.eio.com/repairfaq/sam/laserarg.htm + mixed argon-krypton gas laser @@ -86553,13 +104192,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - MoFlo - MoFlo at TSRI Flow Cytometry Core Facility + MoFlo + MoFlo at TSRI Flow Cytometry Core Facility - A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium. - John Quinn - http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16 - MoFlo + A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium. + John Quinn + http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16 + MoFlo @@ -86584,13 +104223,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - neodymium-YAG laser - Neodymium-YAG Laser in DURIP99 System + neodymium-YAG laser + Neodymium-YAG Laser in DURIP99 System - A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer. - Daniel Schober - John Quinn - neodymium-YAG laser + A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer. + Daniel Schober + John Quinn + neodymium-YAG laser @@ -86605,14 +104244,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - obscuration bar - obscuration bar in a flow cytometer + obscuration bar + obscuration bar in a flow cytometer - An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. - Daniel Schober - Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 - John Quinn - obscuration bar + An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device. + Daniel Schober + Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249 + John Quinn + obscuration bar @@ -86627,13 +104266,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - optical filter - 720 LP filter, 580/30 BP filter + optical filter + 720 LP filter, 580/30 BP filter - An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. - John Quinn - http://en.wikipedia.org/wiki/Optical_filter - optical filter + An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length. + John Quinn + http://en.wikipedia.org/wiki/Optical_filter + optical filter @@ -86660,14 +104299,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - optical subsystem - optical subsystem of a cytometer + optical subsystem + optical subsystem of a cytometer - A device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles. - DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one. - Person: Daniel Schober - John Quinn - optical subsystem + A device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles. + DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one. + Person: Daniel Schober + John Quinn + optical subsystem @@ -86698,13 +104337,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - photodetector - A photomultiplier tube, a photo diode + photodetector + A photomultiplier tube, a photo diode - A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. - John Quinn - http://einstein.stanford.edu/content/glossary/glossary.html - photodetector + A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye. + John Quinn + http://einstein.stanford.edu/content/glossary/glossary.html + photodetector @@ -86713,13 +104352,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - photodiode - Avalanche photodiode + photodiode + Avalanche photodiode - A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer. - John Quinn - http://cyto.mednet.ucla.edu/Protocols/flow.htm - photodiode + A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer. + John Quinn + http://cyto.mednet.ucla.edu/Protocols/flow.htm + photodiode @@ -86746,13 +104385,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - photomultiplier tube - R9647 by manufactured by Hamamatsu + photomultiplier tube + R9647 by manufactured by Hamamatsu - A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect. - John Quinn - http://cyto.mednet.ucla.edu/Protocols/flow.htm - photomultiplier tube + A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect. + John Quinn + http://cyto.mednet.ucla.edu/Protocols/flow.htm + photomultiplier tube @@ -86767,13 +104406,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - piezo electric crystal + piezo electric crystal quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell. John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - think this is natural thing, not a device HP/JF + think this is natural thing, not a device HP/JF piezo electric crystal @@ -86789,14 +104428,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - plate loader - FC 500 plate loader + plate loader + FC 500 plate loader - Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications. - measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future. - John Quinn - http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf - plate loader + Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications. + measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future. + John Quinn + http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf + plate loader @@ -86805,13 +104444,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - preamplifier - Built in preamplifier in a Hamamatsu H9656 PMT + preamplifier + Built in preamplifier in a Hamamatsu H9656 PMT - A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - preamplifier + A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + preamplifier @@ -86820,13 +104459,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - quartz cuvette flow chamber - CVF-Q-10 flow chamber, CV-Q-10 flow chamber + quartz cuvette flow chamber + CVF-Q-10 flow chamber, CV-Q-10 flow chamber - A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells. - John Quinn - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - quartz cuvette flow chamber + A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells. + John Quinn + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + quartz cuvette flow chamber @@ -86835,13 +104474,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - Reflection - Reflection at TSRI Flow Cytometry Core Facility + Reflection + Reflection at TSRI Flow Cytometry Core Facility - A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells. - John Quinn - http://www.i-cyt.com/reflection.htm - Reflection + A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells. + John Quinn + http://www.i-cyt.com/reflection.htm + Reflection @@ -86850,13 +104489,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - cytometer sample tube - sample tube in a cytometer + cytometer sample tube + sample tube in a cytometer - A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - cytometer sample tube + A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + cytometer sample tube @@ -86877,13 +104516,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - sheath tank - LSR2 sheath tank + sheath tank + LSR2 sheath tank - Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - sheath tank + Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + sheath tank @@ -86892,13 +104531,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - short pass filter - 620 SP filter + short pass filter + 620 SP filter - A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm. - John Quinn - http://en.wikipedia.org/wiki/Low-pass_filter - short pass filter + A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm. + John Quinn + http://en.wikipedia.org/wiki/Low-pass_filter + short pass filter @@ -86907,13 +104546,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - solid state laser - Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command + solid state laser + Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command - A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser. - Daniel Schober - http://en.wikipedia.org/wiki/Solid-state_laser - solid state laser + A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser. + Daniel Schober + http://en.wikipedia.org/wiki/Solid-state_laser + solid state laser @@ -86922,12 +104561,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - Somacount + Somacount - A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk. - John Quinn - http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575 - Somacount + A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk. + John Quinn + http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575 + Somacount @@ -86936,13 +104575,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - SomaScope - SomaScope Mark II Automatic Economical + SomaScope + SomaScope Mark II Automatic Economical - The SomaScope is an instrument to quantify somatic cells in milk. - Josef Spidlen - http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10 - SomaScope + The SomaScope is an instrument to quantify somatic cells in milk. + Josef Spidlen + http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10 + SomaScope @@ -86981,14 +104620,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - flow cytometer sorter - BioSorter2000, LSR2 + flow cytometer sorter + BioSorter2000, LSR2 - A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. - John Quinn - Melanie Courtot - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - flow cytometer sorter + A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest. + John Quinn + Melanie Courtot + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + flow cytometer sorter @@ -87009,13 +104648,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - syringe pump - NE-1000 Single Syringe Pump + syringe pump + NE-1000 Single Syringe Pump - Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates. - Person:John Quinn - http://www.answers.com/topic/syringe, 2007-05-11 - syringe pump + Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates. + Person:John Quinn + http://www.answers.com/topic/syringe, 2007-05-11 + syringe pump @@ -87030,14 +104669,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - voltage amplifier - Linear amplifier, log amplifier, microwave amplifier + voltage amplifier + Linear amplifier, log amplifier, microwave amplifier - A voltage amplifier is a device that amplifies the voltage signal. - Frank Gibson - John Quinn - http://en.wiktionary.org/wiki/amplifier - voltage amplifier + A voltage amplifier is a device that amplifies the voltage signal. + Frank Gibson + John Quinn + http://en.wiktionary.org/wiki/amplifier + voltage amplifier @@ -87052,13 +104691,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - waste tank - LSR2 waste tank + waste tank + LSR2 waste tank - Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished. - Person:John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - waste tank + Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished. + Person:John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + waste tank @@ -87073,13 +104712,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - DNA sequencer - ABI 377 DNA Sequencer, ABI 310 DNA Sequencer + DNA sequencer + ABI 377 DNA Sequencer, ABI 310 DNA Sequencer - A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. - Trish Whetzel - MO - DNA sequencer + A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. + Trish Whetzel + MO + DNA sequencer @@ -87100,13 +104739,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - array scanner - GenePix 4200A, GenePix4000B + array scanner + GenePix 4200A, GenePix4000B - An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip - Trish Whetzel - GROUP: MGED Ontology - array scanner + An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip + Trish Whetzel + GROUP: MGED Ontology + array scanner @@ -87121,13 +104760,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - arrayer - BioRobotics Microgrid II TAS, Affymetrix GMS 417 + arrayer + BioRobotics Microgrid II TAS, Affymetrix GMS 417 - A device which deposits biological material onto a substrate in a defined pattern. - Trish Whetzel - MO_697 arrayer - arrayer + A device which deposits biological material onto a substrate in a defined pattern. + Trish Whetzel + MO_697 arrayer + arrayer @@ -87169,14 +104808,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - centrifuge + centrifuge - A device with a rapidly rotating container that applies centrifugal force to its contents - Melanie Courtot - Person: Jennifer Fostel - Trish Whetzel - http://en.wikipedia.org/wiki/Centrifuge - centrifuge + A device with a rapidly rotating container that applies centrifugal force to its contents + Melanie Courtot + Person: Jennifer Fostel + Trish Whetzel + http://en.wikipedia.org/wiki/Centrifuge + centrifuge @@ -87191,14 +104830,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - computer - Apple PowerBook, Dell OptiPlex + computer + Apple PowerBook, Dell OptiPlex - A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. - Melanie Courtot - Trish Whetzel - http://en.wikipedia.org/wiki/Computer - computer + A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. + Melanie Courtot + Trish Whetzel + http://en.wikipedia.org/wiki/Computer + computer @@ -87213,13 +104852,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - heating block - An instrument used to heat and/or maintain material at a set temperature. + heating block + An instrument used to heat and/or maintain material at a set temperature. - A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay - Daniel Schober - MO - heating block + A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay + Daniel Schober + MO + heating block @@ -87234,14 +104873,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - homogenizer - mortar, blender + homogenizer + mortar, blender - A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. - Melanie Courtot - Trish Whetzel - http://en.wikipedia.org/wiki/Homogenizer - homogenizer + A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. + Melanie Courtot + Trish Whetzel + http://en.wikipedia.org/wiki/Homogenizer + homogenizer @@ -87262,13 +104901,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - hybridization chamber - Glass Array Hybridization Cassette + hybridization chamber + Glass Array Hybridization Cassette - A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. - Trish Whetzel - MO_563 hybridization_chamber - hybridization chamber + A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. + Trish Whetzel + MO_563 hybridization_chamber + hybridization chamber @@ -87289,13 +104928,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - hybridization station - Labnet Problot12 + hybridization station + Labnet Problot12 - A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. - Trish Whetzel - MO_497 hybridization station - hybridization station + A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. + Trish Whetzel + MO_497 hybridization station + hybridization station @@ -87310,15 +104949,15 @@ Manual editing of automatically recorded data in an anesthesia information manag - liquid handler - Beckman BioMek 2000 + liquid handler + Beckman BioMek 2000 - A device that is used for automated liquid transfer and handling. - liquid_handling_instrument - MO_868 liquid_handler - DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation. - DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function. - liquid handler + A device that is used for automated liquid transfer and handling. + liquid_handling_instrument + MO_868 liquid_handler + DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG & DS: Capture as function. All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class. The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation. + DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses. TW: This is required by MO. FG: Or as function. + liquid handler @@ -87339,13 +104978,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - oligonucleotide synthesizer - Automated Multiplex Oligonucleotide Synthesizer + oligonucleotide synthesizer + Automated Multiplex Oligonucleotide Synthesizer - An instrument used to chemically synthesize oligonucleotides. - Trish Whetzel - MO - oligonucleotide synthesizer + An instrument used to chemically synthesize oligonucleotides. + Trish Whetzel + MO + oligonucleotide synthesizer @@ -87360,13 +104999,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - sonicator - Sonicator 3000 + sonicator + Sonicator 3000 - A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. - Trish Whetzel - MO - sonicator + A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. + Trish Whetzel + MO + sonicator @@ -87381,14 +105020,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - spectrophotometer - Helios Gamma Spectrophotometer + spectrophotometer + Helios Gamma Spectrophotometer - A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. - Melanie Courtot - Trish Whetzel - MO - spectrophotometer + A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. + Melanie Courtot + Trish Whetzel + MO + spectrophotometer @@ -87409,18 +105048,18 @@ Manual editing of automatically recorded data in an anesthesia information manag - thermal cycler - Piko(tm) 96-well Thermal Cycler + thermal cycler + Piko(tm) 96-well Thermal Cycler - An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. - Melanie Courtot - Trish Whetzel - DNA_amplifier - PCR_machine - Polymerase_Chain_Reaction_ machine - thermocycler - MO - thermal cycler + An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. + Melanie Courtot + Trish Whetzel + DNA_amplifier + PCR_machine + Polymerase_Chain_Reaction_ machine + thermocycler + MO + thermal cycler @@ -87447,13 +105086,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - vacuum dryer - Model 777 Microarray Oven + vacuum dryer + Model 777 Microarray Oven - An instrument which removes liquid by the application of negative pressure, i.e. vacuum. - Trish Whetzel - MO - vacuum dryer + An instrument which removes liquid by the application of negative pressure, i.e. vacuum. + Trish Whetzel + MO + vacuum dryer @@ -87468,15 +105107,15 @@ Manual editing of automatically recorded data in an anesthesia information manag - vortexer - VWR Genie 2 + vortexer + VWR Genie 2 - A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. - Melanie Courtot - Trish Whetzel - vortex_mixer - http://en.wikipedia.org/wiki/Vortex_mixer - vortexer + A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created. + Melanie Courtot + Trish Whetzel + vortex_mixer + http://en.wikipedia.org/wiki/Vortex_mixer + vortexer @@ -87491,13 +105130,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microarray wash station - ArrayIt(r) Microarray Wash Station + microarray wash station + ArrayIt(r) Microarray Wash Station - A device that is used to wash Affymetrix-type arrays. - Trish Whetzel - MO_626 wash_station - microarray wash station + A device that is used to wash Affymetrix-type arrays. + Trish Whetzel + MO_626 wash_station + microarray wash station @@ -87518,16 +105157,16 @@ Manual editing of automatically recorded data in an anesthesia information manag - temperature control bath - VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. + temperature control bath + VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. - A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. - Alan Ruttenburg - Daniel Schober - Frank Gibson - OBI Instrument branch - DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). - temperature control bath + A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. + Alan Ruttenburg + Daniel Schober + Frank Gibson + OBI Instrument branch + DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature). + temperature control bath @@ -87548,15 +105187,15 @@ Manual editing of automatically recorded data in an anesthesia information manag - molecular crosslinker - Stratalinker + molecular crosslinker + Stratalinker - A device that is able to chemically join two or more molecules. - AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly. - Trish Whetzel - molecular crosslinker - MO ?? cannot be found in MO - molecular crosslinker + A device that is able to chemically join two or more molecules. + AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly. + Trish Whetzel + molecular crosslinker + MO ?? cannot be found in MO + molecular crosslinker @@ -87589,13 +105228,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - image cytometer - The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. + image cytometer + The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. - An image_cytometer is an instrument for image-based study or measurement of cells. - Melanie Courtot - http://web.mit.edu/solab/Research/ImageCytometry.html - image cytometer + An image_cytometer is an instrument for image-based study or measurement of cells. + Melanie Courtot + http://web.mit.edu/solab/Research/ImageCytometry.html + image cytometer @@ -87628,12 +105267,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - cytometer + cytometer - A cytometer is an instrument for counting and/or measuring characteristics of cells. - Melanie Courtot - http://medical.merriam-webster.com/medical/cytometer - cytometer + A cytometer is an instrument for counting and/or measuring characteristics of cells. + Melanie Courtot + http://medical.merriam-webster.com/medical/cytometer + cytometer @@ -87654,16 +105293,16 @@ Manual editing of automatically recorded data in an anesthesia information manag - gel tank - CHEF gel box, slab gel box, capillary electrophoresis + gel tank + CHEF gel box, slab gel box, capillary electrophoresis - A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. - Person:Frank Gibson - Person:Kevin Clancy - electrophoresis box - electrophoresis unit - sep:00095 - gel tank + A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. + Person:Frank Gibson + Person:Kevin Clancy + electrophoresis box + electrophoresis unit + sep:00095 + gel tank @@ -87678,20 +105317,20 @@ Manual editing of automatically recorded data in an anesthesia information manag - power supply - A AC/DC transformer that generates the reqired power for an electrophoresis apparatus + power supply + A AC/DC transformer that generates the reqired power for an electrophoresis apparatus - A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time. - Daniel Schober - Frank Gibson - PSU - electrical power supply - power pack - power supply unit - PERSON: Daniel Schober - sep:00093 - was power_pack, maps to SEP electrical_power_supply - power supply + A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time. + Daniel Schober + Frank Gibson + PSU + electrical power supply + power pack + power supply unit + PERSON: Daniel Schober + sep:00093 + was power_pack, maps to SEP electrical_power_supply + power supply @@ -87700,14 +105339,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - fluorometer - laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 + fluorometer + laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 - A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. - Allyson Lister - Kevin Lister - OBI - fluorometer + A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. + Allyson Lister + Kevin Lister + OBI + fluorometer @@ -87734,13 +105373,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - multispectral imaging flow cytometer + multispectral imaging flow cytometer - A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. - Melanie Courtot - MIFC - http://www.amnis.com/ - multispectral imaging flow cytometer + A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations. + Melanie Courtot + MIFC + http://www.amnis.com/ + multispectral imaging flow cytometer @@ -87749,13 +105388,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microarray - An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. + microarray + An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays. - A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. - Daniel Schober - PERSON: Chris Stoeckert - microarray + A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position. + Daniel Schober + PERSON: Chris Stoeckert + microarray @@ -87764,16 +105403,16 @@ Manual editing of automatically recorded data in an anesthesia information manag - DNA microarray - Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 + DNA microarray + Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 - A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. - PERSON: Daniel Schober - PERSON: Frank Gibson - DNA Chip - DNA-array - Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 - DNA microarray + A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample. + PERSON: Daniel Schober + PERSON: Frank Gibson + DNA Chip + DNA-array + Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03 + DNA microarray @@ -87782,13 +105421,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - protein microarray - The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. + protein microarray + The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. - A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. - Daniel Schober - PERSON: Daniel Schober - protein microarray + A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. + Daniel Schober + PERSON: Daniel Schober + protein microarray @@ -87803,12 +105442,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - droplet sorter + droplet sorter - A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. - OBI Instrument branch - OBI Instrument branch - droplet sorter + A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal. + OBI Instrument branch + OBI Instrument branch + droplet sorter @@ -87817,13 +105456,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - water bath - A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. + water bath + A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. - A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). - Daniel Schober - PERSON: Daniel Schober - water bath + A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). + Daniel Schober + PERSON: Daniel Schober + water bath @@ -87832,13 +105471,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - oil bath - An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period. + oil bath + An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period. - An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample). - Daniel Schober - PERSON: Daniel Schober - oil bath + An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample). + Daniel Schober + PERSON: Daniel Schober + oil bath @@ -87853,13 +105492,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - digital-to-analog converter - A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound. + digital-to-analog converter + A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound. - A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal. - Daniel Schober - PERSON: Daniel Schober - digital-to-analog converter + A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal. + Daniel Schober + PERSON: Daniel Schober + digital-to-analog converter @@ -87880,13 +105519,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microtome - PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. + microtome + PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7. - A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. - PERSON: Phillippe Rocca-Serra - PERSON: Daniel Schober - microtome + A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand. + PERSON: Phillippe Rocca-Serra + PERSON: Daniel Schober + microtome @@ -87907,13 +105546,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microscope - PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6 + microscope + PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6 - A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) - PERSON: Phillippe Rocca-Serra - wikipedia - microscope + A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) + PERSON: Phillippe Rocca-Serra + wikipedia + microscope @@ -87928,13 +105567,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - microscope slide - PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. + microscope slide + PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. - A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument - PERSON: Phillippe Rocca-Serra - OBI biomaterial branch - microscope slide + A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument + PERSON: Phillippe Rocca-Serra + OBI biomaterial branch + microscope slide @@ -87949,14 +105588,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - animal cage - PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice. + animal cage + PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice. - A processed material which has the function to define a bounded habitat which is amenable to keeping animals. - PERSON: Phillippe Rocca-Serra - laboratory cage - OBI biomaterial branch - animal cage + A processed material which has the function to define a bounded habitat which is amenable to keeping animals. + PERSON: Phillippe Rocca-Serra + laboratory cage + OBI biomaterial branch + animal cage @@ -87964,6 +105603,7 @@ Manual editing of automatically recorded data in an anesthesia information manag + @@ -87973,11 +105613,12 @@ Manual editing of automatically recorded data in an anesthesia information manag study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. - PERSON: Chris Stoeckert + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. + PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. + study design @@ -87987,14 +105628,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - clinical study design - PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. + clinical study design + PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale. - Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] - The definition needs to be extended to other things than simply patients - PlanAndPlannedProcess Branch - Clinical Research Glossary Version 4.0 CDICS glossary group - clinical study design + Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach] + The definition needs to be extended to other things than simply patients + PlanAndPlannedProcess Branch + Clinical Research Glossary Version 4.0 CDICS glossary group + clinical study design @@ -88003,13 +105644,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - repeated measure design - PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. + repeated measure design + PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations. - a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs - PlanAndPlannedProcess Branch - http://www.holah.karoo.net/experimentaldesigns.htm - repeated measure design + a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs + PlanAndPlannedProcess Branch + http://www.holah.karoo.net/experimentaldesigns.htm + repeated measure design @@ -88018,13 +105659,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - cross over design - PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. + cross over design + PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity. - a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control - Philippe Rocca-Serra - (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) - cross over design + a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control + Philippe Rocca-Serra + (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html) + cross over design @@ -88033,12 +105674,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - n-to-1 design + n-to-1 design - N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). - Philippe Rocca-Serra - Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) - n-to-1 design + N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993). + Philippe Rocca-Serra + Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm) + n-to-1 design @@ -88047,13 +105688,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - matched pairs design - PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. + matched pairs design + PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs. - A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. - Philippe Rocca-Serra - http://www.holah.karoo.net/experimentaldesigns.htm - matched pairs design + A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment. + Philippe Rocca-Serra + http://www.holah.karoo.net/experimentaldesigns.htm + matched pairs design @@ -88062,14 +105703,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - parallel group design - PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. + parallel group design + PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR. - A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment - Philippe Rocca-Serra - independent measure design - http://www.holah.karoo.net/experimentaldesigns.htm - parallel group design + A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment + Philippe Rocca-Serra + independent measure design + http://www.holah.karoo.net/experimentaldesigns.htm + parallel group design @@ -88078,13 +105719,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - randomized complete block design - http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) + randomized complete block design + http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) - A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. - Philippe Rocca-Serra - http://www.tufts.edu/~gdallal/ranblock.htm - randomized complete block design + A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. + Philippe Rocca-Serra + http://www.tufts.edu/~gdallal/ranblock.htm + randomized complete block design @@ -88093,13 +105734,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - balanced incomplete block design - PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. + balanced incomplete block design + PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice. - balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' - Philippe Rocca-Serra - http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html - balanced incomplete block design + balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i' + Philippe Rocca-Serra + http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html + balanced incomplete block design @@ -88108,13 +105749,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - loop design - PMID: 12933549 + loop design + PMID: 12933549 - A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design - Philippe Rocca-Serra on behalf of MO - MO_912 - loop design + A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design + Philippe Rocca-Serra on behalf of MO + MO_912 + loop design @@ -88123,13 +105764,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - reference design - PMID: 12933549 + reference design + PMID: 12933549 - A reference experiment design type is where all samples are compared to a common reference. - Philippe Rocca-Serra on behalf of MO - MO_699 - reference design + A reference experiment design type is where all samples are compared to a common reference. + Philippe Rocca-Serra on behalf of MO + MO_699 + reference design @@ -88138,13 +105779,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - latin square design - PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. + latin square design + PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. - Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. - Philippe Rocca-Serra - Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and - latin square design + Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once. + Philippe Rocca-Serra + Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and + latin square design @@ -88153,14 +105794,14 @@ Manual editing of automatically recorded data in an anesthesia information manag - graeco latin square design - PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. + graeco latin square design + PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes. - Greco-Latin square design is a study design which relates to Latin square design - Philippe Rocca-Serra - Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and - only 2 articles in pubmed ->probably irrelevant - graeco latin square design + Greco-Latin square design is a study design which relates to Latin square design + Philippe Rocca-Serra + Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and + only 2 articles in pubmed ->probably irrelevant + graeco latin square design @@ -88169,13 +105810,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - hyper graeco latin square design + hyper graeco latin square design - PRS to do - Philippe Rocca-Serra - Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and - no example found in pubmed->not in use in the community - hyper graeco latin square design + PRS to do + Philippe Rocca-Serra + Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and + no example found in pubmed->not in use in the community + hyper graeco latin square design @@ -88184,12 +105825,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. + factorial design + PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine. - factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. - Philippe Rocca-Serra - http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) - factorial design + factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable. + Philippe Rocca-Serra + http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment) + factorial design @@ -88198,13 +105840,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - 2x2 factorial design - PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. + 2x2 factorial design + PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. - a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors - Philippe Rocca-Serra - PMID: 17561240 - 2x2 factorial design + a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors + Philippe Rocca-Serra + PMID: 17561240 + 2x2 factorial design @@ -88213,12 +105855,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - fractional factorial design + fractional factorial design - A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run - Philippe Rocca-Serra - http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control - fractional factorial design + A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run + Philippe Rocca-Serra + http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control + fractional factorial design @@ -88227,13 +105869,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - dye swap design - PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. + dye swap design + PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. - An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip - Philippe Rocca-Serra on behalf of MO - MO_858 - dye swap design + An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip + Philippe Rocca-Serra on behalf of MO + MO_858 + dye swap design @@ -88242,12 +105884,12 @@ Manual editing of automatically recorded data in an anesthesia information manag - replicate design + replicate design - A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. - Philippe Rocca-Serra on behalf of MO - MO_885 - replicate design + A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. + Philippe Rocca-Serra on behalf of MO + MO_885 + replicate design @@ -88256,13 +105898,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - self vs self design - PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. + self vs self design + PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design. - A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. - Philippe Rocca-Serra on behalf of MO - MO_490 - self vs self design + A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. + Philippe Rocca-Serra on behalf of MO + MO_490 + self vs self design @@ -88271,13 +105913,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - time series design - PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. + time series design + PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources. - Groups of assays that are related as part of a time series. - Philippe Rocca-Serra on behalf of MO - MO_887 - time series design + Groups of assays that are related as part of a time series. + Philippe Rocca-Serra on behalf of MO + MO_887 + time series design @@ -88439,7 +106081,7 @@ defines and states the requirements (positive or negative) for an entity to be c adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient is process in which a material substance is added to a cell culture - renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms + renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms Bjoern Peters IEDB adding substance to cell culture @@ -88468,12 +106110,13 @@ defines and states the requirements (positive or negative) for an entity to be c + tumor grading - An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. - Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney - grading of tumor - OBI branch derived; submitted by MO - tumor grading + An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. + Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney + grading of tumor + OBI branch derived; submitted by MO + tumor grading @@ -88482,14 +106125,15 @@ defines and states the requirements (positive or negative) for an entity to be c + obsolete performing a clinical assessment - A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. - PlanAndPlannedProcess Branch - clinical diagnosis - OBI branch derived + A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. + PlanAndPlannedProcess Branch + clinical diagnosis + OBI branch derived - https://github.com/obi-ontology/obi/issues/623 - obsolete performing a clinical assessment + https://github.com/obi-ontology/obi/issues/623 + obsolete performing a clinical assessment true @@ -88560,7 +106204,7 @@ defines and states the requirements (positive or negative) for an entity to be c enlisting familiy members of HIV patients into a study A planned process with the objective to obtain a population of human subjects to participate in an investigation by determining eligibility of subjects and obtaining informed consent. - As with group assignment, should the specified output here be an organism which bears a role + As with group assignment, should the specified output here be an organism which bears a role Bjoern Peters IEDB criteria come from plan / clinical trial branch @@ -88650,7 +106294,7 @@ defines and states the requirements (positive or negative) for an entity to be c A protocol application in which an organism is intentionally put to death difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing. Jennifer Fostel - Philippe Rocca-Serra + Philippe Rocca-Serra death status type euthanisia life termination @@ -88721,17 +106365,17 @@ defines and states the requirements (positive or negative) for an entity to be c administering substance in vivo - Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells + Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally - A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. - 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 + A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance. + 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 Different routes and means of administration should go as children underneath this Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/ needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor. Bjoern Peters - Person:Bjoern Peters + Person:Bjoern Peters IEDB administering substance in vivo @@ -88767,10 +106411,10 @@ https://sourceforge.net/p/obi/obi-terms/738/ acquisition - Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. + Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. the planned process of gaining possession of a continuant - 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. + 5/31/2012 - OBI workshop: This process is not implying ownership of the material / information. Following OBI call November 2012,5th: addition of a restriction to acquisition class to capture the need of having selection criteria Relates to the creation of a class 'selection rule' @@ -88812,10 +106456,10 @@ Relates to the creation of a class 'selection rule' Acquiring 50 C57BL/6 mice bred in the animal facility of the institute as a service to investigators. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI. An acquisition in which possession of a material entity is gained. - The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation + The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from specimen creation This excludes processes that create or change materials, such as material transformations. Bjoern Peters, Alan Ruttenberg, Helen Parkinson - material procurement + material procurement IEDB material acquisition @@ -88889,7 +106533,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ An acquisition in which possession of information is gained. This excludes processes that create or change information, such as assays and data transformations. Bjoern Peters - data collection + data collection OBI branch derived information acquisition @@ -88960,8 +106604,8 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ group assignment is a process which has an organism as specified input and during which a role is assigned Philippe Rocca-Serra - cohort assignment - study assignment + cohort assignment + study assignment OBI Plan group assignment @@ -88996,7 +106640,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ 2 - pooling specimens + pooling specimens http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points physical combination of several instances of like material @@ -89036,12 +106680,13 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present + assay detecting a molecular label + Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present - An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached - Matthew Brush - OBI developer call, 3-12-12 - assay detecting a molecular label + An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached + Matthew Brush + OBI developer call, 3-12-12 + assay detecting a molecular label @@ -89126,15 +106771,16 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated + histological assay + the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated - An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement. - Adam Witney - Helen Parkinson - histology - histopathology - OBI branch derived - histological assay + An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement. + Adam Witney + Helen Parkinson + histology + histopathology + OBI branch derived + histological assay @@ -89318,12 +106964,13 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - the detection of phycoerytherin by means of flow cytometry + substance detection assay + the detection of phycoerytherin by means of flow cytometry - An assay that detects a specified substance - Kevin Clancy - OBI branch derived - substance detection assay + An assay that detects a specified substance + Kevin Clancy + OBI branch derived + substance detection assay @@ -89344,12 +106991,13 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection + longitudinal mass measurement assay + The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection - An assay that measures the mass of a material at two or more time points - Helen Parkinson - OBI branch derived - longitudinal mass measurement assay + An assay that measures the mass of a material at two or more time points + Helen Parkinson + OBI branch derived + longitudinal mass measurement assay @@ -89408,7 +107056,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) - It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process. + It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process. We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope PERSON:Kevin Clancy OBI branch derived @@ -89523,12 +107171,14 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. - A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. - IEDB - ELISPOT assay - IEDB - enzyme-linked immunospot assay + enzyme-linked immunospot assay + Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell. + + A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest. + IEDB + ELISPOT assay + IEDB + enzyme-linked immunospot assay @@ -89677,7 +107327,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing PlanAndPlannedProcess Branch - cell culture passaging + cell culture passaging OBI branch derived An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. cell culture splitting @@ -89718,7 +107368,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay PERSON:Matthew Brush - labeling + labeling OBI developer call, 3-12-12 addition of molecular label @@ -89768,7 +107418,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - synthesis + synthesis making cDNA from nucleotides using RNA as a template the construction of a biomaterial from simpler biomaterials @@ -89906,11 +107556,13 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. - An assay that determines the 3-dimensional configuration of an input material. - IEDB - IEDB - 3D structure determination assay + 3D structure determination assay + The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein. + + An assay that determines the 3-dimensional configuration of an input material. + IEDB + IEDB + 3D structure determination assay @@ -90065,12 +107717,13 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template + sequencing assay + The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template - An assay the uses chemical or biochemical means to infer the sequence of a biomaterial - PlanAndPlannedProcess Branch - OBI branch derived - sequencing assay + An assay the uses chemical or biochemical means to infer the sequence of a biomaterial + PlanAndPlannedProcess Branch + OBI branch derived + sequencing assay @@ -90079,7 +107732,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - vector mediated amplification + vector mediated amplification E coli expressing the gene for M avium p35 were cultured in order to produce p35. The process of creating a copy of some biological entity in cell culture @@ -90121,7 +107774,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input PERSON:Kevin Clancy - Philippe Rocca-Serra + Philippe Rocca-Serra OBI branch derived DNA polymerase amplification @@ -90437,7 +108090,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ vector mediated expression - Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity. + Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity. vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector needs defined relationship to cell culture @@ -90496,7 +108149,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material pa_branch (Alan, Randi, Kevin, Jay, Bjoern) - molecular cloning + molecular cloning OBI branch derived recombinant vector cloning @@ -90507,12 +108160,13 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + obsolete_defined processes - Place holder class, see editor note - PlanAndPlannedProcess Branch - OBI branch derived + Place holder class, see editor note + PlanAndPlannedProcess Branch + OBI branch derived - obsolete_defined processes + obsolete_defined processes true @@ -90647,9 +108301,9 @@ Isolation of proliferation factor of immature T-cell clone in concanavalin A-sti A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension PERSON: Helen Parkinson - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra GROUP: CEBS - GROUP: OBI Biomaterial Branch + GROUP: OBI Biomaterial Branch cell pellet @@ -90704,14 +108358,14 @@ addition of has_role restriction cell lysate - The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932 + The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932 a cell lysate is a material entity which is output of a cell lysis process PRS:22-02-2008: is a material which has output_role during lysis protocol-application. old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process PERSON: Susanna Sansone lysate - lysed material + lysed material GROUP: PSI cell lysate @@ -90764,7 +108418,7 @@ Possible ecological risks of transgenic organism release when transgenes affect a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra GROUP:IEDB transgenic organism @@ -90791,7 +108445,7 @@ Possible ecological risks of transgenic organism release when transgenes affect A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide PERSON: Helen Parkinson - PERSON: Philippe Rocca-Serra + PERSON: Philippe Rocca-Serra whole mount sample GROUP: OBI PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity @@ -90827,7 +108481,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - epitope + epitope a material entity bearing the epitope role IEDB @@ -90841,12 +108495,13 @@ Possible ecological risks of transgenic organism release when transgenes affect + obsolete_occurrence of disease - An occurrence of disease is a process involving pathologic changes within an organism - IEDB - IEDB + An occurrence of disease is a process involving pathologic changes within an organism + IEDB + IEDB - obsolete_occurrence of disease + obsolete_occurrence of disease true @@ -90890,7 +108545,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - host exposure to infectious agent + host exposure to infectious agent a process in which an infectious agent comes into physical contact with a host organism. IEDB @@ -90920,7 +108575,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - administration in vivo with infectious agent + administration in vivo with infectious agent is an administration of an infectious agent to a host organism IEDB @@ -90962,7 +108617,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - occurrence of infectious disease + occurrence of infectious disease Is an occurrence of a disease caused by an infection IEDB @@ -90982,11 +108637,11 @@ Possible ecological risks of transgenic organism release when transgenes affect - disposition to cause an allergic reaction + disposition to cause an allergic reaction The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease. IEDB - allergenic disposition + allergenic disposition IEDB disposition to cause an allergic reaction @@ -91003,7 +108658,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - allergic reaction + allergic reaction an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen) IEDB @@ -91029,7 +108684,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - occurrence of allergy + occurrence of allergy The process of an allergic disease occurring in an organism. IEDB @@ -91068,11 +108723,13 @@ Possible ecological risks of transgenic organism release when transgenes affect - An enzyme-linked immunospot assay that detects interleukin-2 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-2 production by T cells + ELISPOT assay measuring epitope specific interleukin-2 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-2 production by T cells @@ -91107,7 +108764,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - epitope binding by adaptive immune receptor + epitope binding by adaptive immune receptor is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding. IEDB @@ -91127,7 +108784,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - Immunization in vivo + Immunization in vivo Process of administering an object playing the role of immunogen to a living organism IEDB @@ -91161,7 +108818,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - adaptive immune effector function + adaptive immune effector function A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience. IEDB @@ -91175,9 +108832,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - living with infected household contact + living with infected household contact - a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent + a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent IEDB IEDB living with infected household contact @@ -91189,9 +108846,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - living in endemic area + living in endemic area - a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely + a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely IEDB IEDB living in endemic area @@ -91203,9 +108860,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - pathogen release in laboratory accident + pathogen release in laboratory accident - a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent + a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent IEDB IEDB pathogen release in laboratory accident @@ -91241,7 +108898,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - Immunization in vitro + Immunization in vitro Process of administering an object playing the role of immunogen to a cell culture IEDB @@ -91267,7 +108924,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - infection process + infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB @@ -91290,7 +108947,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - adaptive immune receptor + adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB @@ -91310,7 +108967,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - immunogen + immunogen a material entity bearing the immunogen role IEDB @@ -91360,7 +109017,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - environmental exposure to infectious agent + environmental exposure to infectious agent Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent IEDB @@ -91384,11 +109041,11 @@ Possible ecological risks of transgenic organism release when transgenes affect - host of immune response - A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. + host of immune response + A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. An organism in which an immune response process occurs. - In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation. + In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation. IEDB IEDB host of immune response @@ -91400,9 +109057,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - 293-T cell line + 293-T cell line - A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication. + A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5008.html @@ -91415,9 +109072,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - C1R cell line + C1R cell line - A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)). + A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)). IEDB IEDB C1R cell line @@ -91445,7 +109102,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - experimental infection of cell culture + experimental infection of cell culture is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture IEDB @@ -91459,9 +109116,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - EL-4 cell line + EL-4 cell line - A cell line derived from mouse (C57BL/6N) lymphoma cells. + A cell line derived from mouse (C57BL/6N) lymphoma cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1160.html @@ -91474,9 +109131,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - HeLa cell culture + HeLa cell culture - A cell line derived from human cervical cancer cells. + A cell line derived from human cervical cancer cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1597.html @@ -91489,9 +109146,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - JAWS II cell line + JAWS II cell line - A cell line derived from mouse dendritic cells. + A cell line derived from mouse dendritic cells. IEDB IEDB http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology @@ -91510,7 +109167,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - antigen + antigen is a material entity that has the antigen role IEDB @@ -91524,9 +109181,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - Jurkat cell line + Jurkat cell line - A cell line derived from human T cells. + A cell line derived from human T cells. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5296.html @@ -91539,9 +109196,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - JY cell line + JY cell line - The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) + The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) IEDB IEDB JY cell line @@ -91572,11 +109229,13 @@ Possible ecological risks of transgenic organism release when transgenes affect - A T cell epitope assay that measures the binding of T cell receptor to an epitope. - IEDB - IEDB - T cell binding|any method - assay measuring binding of a T cell epitope:MHC:TCR complex + assay measuring binding of a T cell epitope:MHC:TCR complex + + A T cell epitope assay that measures the binding of T cell receptor to an epitope. + IEDB + IEDB + T cell binding|any method + assay measuring binding of a T cell epitope:MHC:TCR complex @@ -91585,9 +109244,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - RMA cell line + RMA cell line - A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface. + A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface. IEDB IEDB RMA cell line @@ -91599,9 +109258,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - T2 cell line + T2 cell line - A human T-B lymphoblastoid hybrid cell line + A human T-B lymphoblastoid hybrid cell line IEDB IEDB http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1992&Template=cellBiology @@ -91614,7 +109273,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - infectious disease + infectious disease is a disease caused by an infectious agent IEDB @@ -91644,9 +109303,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - lymph node cell specimen + lymph node cell specimen - A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. + A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB lymph node cell specimen @@ -91668,9 +109327,9 @@ Possible ecological risks of transgenic organism release when transgenes affect - cultured adherent cell population + cultured adherent cell population - A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role. + A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role. MHB 3-27-13: Following CLO alignment efforts, propose to update definition to read: "A cultured cell population comprised of cells that are able to grow attached to a solid substrate provided by tissue culture flasks or plates". The current definition seems to describe a more specific type of adherent culture of immunological origin as needed by IEDB. MHB 3-5-13: Need to review axiom on this class in light of clarification that it refers to a cell line sample, and not an entire line. Not every population of adhernet cells is the output of an isolation process. @@ -91696,9 +109355,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured PBMC cell population + cultured PBMC cell population - A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types). + A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types). IEDB PBMC cell culture sample IEDB @@ -91717,11 +109376,11 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - disposition to be bound by an adaptive immune receptor + disposition to be bound by an adaptive immune receptor Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor. IEDB - epitope disposition + epitope disposition IEDB disposition to be bound by an adaptive immune receptor @@ -91732,7 +109391,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - organ harvesting + organ harvesting The process of removing an organ from its source organism IEDB @@ -91766,9 +109425,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD3+ T cell population + cultured CD3+ T cell population - A T cell population characterized by expressing the CD3 molecule on its surface. + A T cell population characterized by expressing the CD3 molecule on its surface. IEDB CD3+ T cell culture sample IEDB @@ -91805,9 +109464,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD3- T cell population + cultured CD3- T cell population - A T cell population characterized by not expressing the CD3 molecule on its surface. + A T cell population characterized by not expressing the CD3 molecule on its surface. IEDB CD3- T cell culture sample IEDB @@ -91820,7 +109479,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - allergy + allergy is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect IEDB @@ -91858,9 +109517,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD4- T cell population + cultured CD4- T cell population - A T cell population characterized by not expressing the CD4 molecule on its surface. + A T cell population characterized by not expressing the CD4 molecule on its surface. IEDB CD4- T cell culture sample IEDB @@ -91897,9 +109556,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD8- T cell population + cultured CD8- T cell population - A T cell population characterized by not expressing the CD8 molecule on its surface. + A T cell population characterized by not expressing the CD8 molecule on its surface. IEDB CD8- T cell culture sample IEDB @@ -91944,9 +109603,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured CD4-/CD8- T cell population + cultured CD4-/CD8- T cell population - A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. + A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. IEDB CD4-/CD8- T cell culture sample IEDB @@ -91959,7 +109618,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cancer + cancer A disease characterized by abnormal and uncontrolled cell division IEDB @@ -91973,7 +109632,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - autoimmune disease + autoimmune disease Is a disease characterized by an immune response of an organism against parts of itself IEDB @@ -91987,13 +109646,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it + obsolete_disease - placeholder to be imported from disease ontology - IEDB - IEDB + placeholder to be imported from disease ontology + IEDB + IEDB - obsolete_disease + obsolete_disease true @@ -92013,7 +109673,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-2 release by T cells + epitope specific IL-2 release by T cells A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope. IEDB @@ -92073,7 +109733,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - MHC:epitope complex binding to TCR + MHC:epitope complex binding to TCR a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule. IEDB @@ -92112,11 +109772,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ELISPOT - ELISPOT assay measuring epitope specific interferon-gamma production by T cells + ELISPOT assay measuring epitope specific interferon-gamma production by T cells + + An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ELISPOT + ELISPOT assay measuring epitope specific interferon-gamma production by T cells @@ -92125,9 +109787,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - exposure resulting in immune reactivity + exposure resulting in immune reactivity - a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity + a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity IEDB IEDB exposure resulting in immune reactivity @@ -92139,7 +109801,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - immunogen role + immunogen role any entity capable of eliciting an immune response when introduced to components of the immune system IEDB @@ -92166,10 +109828,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - host of immune response role + host of immune response role is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host. - 03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO. + 03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO. IEDB IEDB host of immune response role @@ -92203,7 +109865,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - effector T cell function + effector T cell function The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex. IEDB @@ -92233,13 +109895,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - antigen presentation function + antigen presentation function a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface. IEDB APC IEDB - should add a reference to the antigen processing and presentation process. + should add a reference to the antigen processing and presentation process. antigen presentation function @@ -92249,7 +109911,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - restricting MHC role + restricting MHC role The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell. IEDB @@ -92263,14 +109925,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - donor - A T cell line from a PPD(+) donor. + donor + A T cell line from a PPD(+) donor. A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. IEDB - donor role + donor role IEDB - Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. + Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. donor @@ -92280,10 +109942,10 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - immune epitope carrier role + immune epitope carrier role A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity. - 03/21/2010, BP: surveying the literature, this seems to be a messy term. Need to clarify what material entities can be carriers, and if only immunogenicity (not antigenicity) is effected by their presence. + 03/21/2010, BP: surveying the literature, this seems to be a messy term. Need to clarify what material entities can be carriers, and if only immunogenicity (not antigenicity) is effected by their presence. IEDB IEDB immune epitope carrier role @@ -92307,11 +109969,11 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - adjuvant role + adjuvant role Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response. IEDB - adjuvent role + adjuvent role IEDB adjuvant role @@ -92328,7 +109990,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - disposition to infect an organism + disposition to infect an organism Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease IEDB @@ -92407,8 +110069,8 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - immunization - Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope). + immunization + Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope). The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope. IEDB @@ -92428,7 +110090,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - blood harvesting + blood harvesting A material separation where blood is taken from an organism. IEDB @@ -92442,9 +110104,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - L cell line + L cell line - A cell line derived from mouse fibroblasts. + A cell line derived from mouse fibroblasts. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl3075.html @@ -92477,13 +110139,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured antigen presenting cell population - A culture of PBMCs. A culture of Hela cells. + cultured antigen presenting cell population + A culture of PBMCs. A culture of Hela cells. - a cell culture including cells that have an antigen presentation function + a cell culture including cells that have an antigen presentation function antigen presenting cell culture sample - IEDB - cultured antigen presenting cell population + IEDB + cultured antigen presenting cell population @@ -92512,14 +110174,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - cultured effector T cell population - A culture of cytotoxic CD8+ T cells. + cultured effector T cell population + A culture of cytotoxic CD8+ T cells. - A cell culture including cells that have an effector T cell function + A cell culture including cells that have an effector T cell function culture of effector T cells effector T cell culture sample - IEDB - cultured effector T cell population + IEDB + cultured effector T cell population @@ -92534,14 +110196,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - material to be added - A mixture of peptides that is being added into a cell culture. + material to be added + A mixture of peptides that is being added into a cell culture. - a material that is added to another one in a material combination process - 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export - 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes - IEDB - material to be added + a material that is added to another one in a material combination process + 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export + 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes + IEDB + material to be added @@ -92556,13 +110218,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - target of material addition - A cell culture into which a mixture of peptides is being added. + target of material addition + A cell culture into which a mixture of peptides is being added. - A material entity into which another is being added in a material combinatino process - 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. - IEDB - target of material addition + A material entity into which another is being added in a material combinatino process + 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export. + IEDB + target of material addition @@ -92571,7 +110233,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - environmental proximity to infectious agent + environmental proximity to infectious agent Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result IEDB @@ -92585,9 +110247,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - contact to pathogen carrying biological vector + contact to pathogen carrying biological vector - a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result + a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result IEDB IEDB contact to pathogen carrying biological vector @@ -92615,9 +110277,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - splenocyte specimen + splenocyte specimen - A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. + A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types. IEDB IEDB splenocyte specimen @@ -92629,9 +110291,9 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - P815 cell line + P815 cell line - A cell line derived from mouse mastocytoma. + A cell line derived from mouse mastocytoma. IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5244.html @@ -92650,7 +110312,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - assay antigen role + assay antigen role Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. see OBI_1110120 below IEDB @@ -92664,7 +110326,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - pathologic process + pathologic process abnormal, harmful processes caused by or associated with a disease IEDB @@ -92697,11 +110359,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|binding assay - assay measuring qualitative binding of a T cell epitope:MHC:TCR complex + assay measuring qualitative binding of a T cell epitope:MHC:TCR complex + + An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|binding assay + assay measuring qualitative binding of a T cell epitope:MHC:TCR complex @@ -92749,11 +110413,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. - IEDB - IEDB - ligand presentation|any method - assay measuring MHC ligand processing and presentation + assay measuring MHC ligand processing and presentation + + A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them. + IEDB + IEDB + ligand presentation|any method + assay measuring MHC ligand processing and presentation @@ -92781,11 +110447,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A MHC ligand assay that detects the binding of a ligand to an MHC molecule. - IEDB - IEDB - MHC binding|any method - assay measuring binding of a MHC:ligand complex + assay measuring binding of a MHC:ligand complex + + A MHC ligand assay that detects the binding of a ligand to an MHC molecule. + IEDB + IEDB + MHC binding|any method + assay measuring binding of a MHC:ligand complex @@ -92813,11 +110481,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A B cell epitope assay that measures the binding of an antibody receptor to an epitope. - IEDB - IEDB - antibody binding|any method - assay measuring binding of a B cell epitope:antibody complex + assay measuring binding of a B cell epitope:antibody complex + + A B cell epitope assay that measures the binding of an antibody receptor to an epitope. + IEDB + IEDB + antibody binding|any method + assay measuring binding of a B cell epitope:antibody complex @@ -92872,11 +110542,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An assay that detects the binding of an epitope to an adaptive immune receptor, or an immune process resulting from such a binding event, or characterizes the structrue of the complex resulting from such a binding event. - IEDB - IEDB - immune epitope assay - immune epitope assay + immune epitope assay + + An assay that detects the binding of an epitope to an adaptive immune receptor, or an immune process resulting from such a binding event, or characterizes the structrue of the complex resulting from such a binding event. + IEDB + IEDB + immune epitope assay + immune epitope assay @@ -92910,11 +110582,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A T cell epitope assay that detects cytokine production by T cells. - IEDB - IEDB - cytokine release|biological activity - assay measuring epitope specific cytokine production by T cells + assay measuring epitope specific cytokine production by T cells + + A T cell epitope assay that detects cytokine production by T cells. + IEDB + IEDB + cytokine release|biological activity + assay measuring epitope specific cytokine production by T cells @@ -92925,35 +110599,36 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - - - - - - - - - + - + + + + + + + + + + + - A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. - IEDB - IEDB - cytotoxicity|biological activity - biological activity assay measuring epitope specific T cell killing + assay measuring epitope specific T cell killing + + A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. + IEDB + IEDB + cytotoxicity|biological activity + assay measuring epitope specific T cell killing @@ -92964,35 +110639,36 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - - - - - - - - - - + - + + + + + + + + + + + - A T cell epitope dependent biological activity assay that detects T cell proliferation. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - proliferation|biological activity - biological activity assay measuring epitope specific proliferation of T cells + assay measuring epitope specific proliferation of T cells + + A T cell epitope dependent biological activity assay that detects T cell proliferation. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + proliferation|biological activity + assay measuring epitope specific proliferation of T cells @@ -93001,13 +110677,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - CD8 receptor + CD8 receptor - A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. - This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. - CD8 - WEB: http://en.wikipedia.org/wiki/CD8 - CD8 receptor + A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. + This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. + CD8 + WEB: http://en.wikipedia.org/wiki/CD8 + CD8 receptor @@ -93018,26 +110694,50 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A T cell epitope specific killing assay performed in vitro that uses a chromium release assay. - IEDB - IEDB - cytotoxicity|51 chromium - 51 chromium assay measuring epitope specific T cell killing + 51 chromium assay measuring epitope specific T cell killing + + A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC. + IEDB + IEDB + cytotoxicity|51 chromium + 51 chromium assay measuring epitope specific T cell killing @@ -93071,11 +110771,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ELISA - ELISA measuring epitope specific interferon-gamma production by T cells + ELISA measuring epitope specific interferon-gamma production by T cells + + An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ELISA + ELISA measuring epitope specific interferon-gamma production by T cells @@ -93109,11 +110811,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ELISA - ELISA measuring epitope specific interleukin-2 production by T cells + ELISA measuring epitope specific interleukin-2 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ELISA + ELISA measuring epitope specific interleukin-2 production by T cells @@ -93147,11 +110851,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ELISA - ELISA measuring epitope specific interleukin-4 production by T cells + ELISA measuring epitope specific interleukin-4 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ELISA + ELISA measuring epitope specific interleukin-4 production by T cells @@ -93185,11 +110891,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|ELISA - ELISA measuring epitope specific interleukin-5 production by T cells + ELISA measuring epitope specific interleukin-5 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|ELISA + ELISA measuring epitope specific interleukin-5 production by T cells @@ -93223,11 +110931,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects tumor necrosis factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|ELISA - ELISA measuring epitope specific tumor necrosis factor production by T cells + ELISA measuring epitope specific tumor necrosis factor alpha production by T cells + + An enzyme-linked immunosorbent assay that detects tumor necrosis factor alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|ELISA + ELISA measuring epitope specific tumor necrosis factor alpha production by T cells @@ -93261,11 +110971,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ELISA - ELISA measuring epitope specific interleukin-10 production by T cells + ELISA measuring epitope specific interleukin-10 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ELISA + ELISA measuring epitope specific interleukin-10 production by T cells @@ -93299,11 +111011,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects granulocyte macrophage colony stimulating factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - GM-CSF release|ELISA - ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells + + An enzyme-linked immunosorbent assay that detects granulocyte macrophage colony stimulating factor production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + GM-CSF release|ELISA + ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells @@ -93337,11 +111051,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-6 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|ELISA - ELISA measuring epitope specific interleukin-6 production by T cells + ELISA measuring epitope specific interleukin-6 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-6 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|ELISA + ELISA measuring epitope specific interleukin-6 production by T cells @@ -93375,11 +111091,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISA - ELISA measuring epitope specific interleukin-13 production by T cells + ELISA measuring epitope specific interleukin-13 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ELISA + ELISA measuring epitope specific interleukin-13 production by T cells @@ -93413,11 +111131,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-12 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|ELISA - ELISA measuring epitope specific interleukin-12 production by T cells + ELISA measuring epitope specific interleukin-12 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-12 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|ELISA + ELISA measuring epitope specific interleukin-12 production by T cells @@ -93451,11 +111171,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-1 beta production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|ELISA - ELISA measuring epitope specific interleukin-1 beta production by T cells + ELISA measuring epitope specific interleukin-1 beta production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-1 beta production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|ELISA + ELISA measuring epitope specific interleukin-1 beta production by T cells @@ -93489,11 +111211,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ELISA - ELISA measuring epitope specific interleukin-17 production by T cells + ELISA measuring epitope specific interleukin-17 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|ELISA + ELISA measuring epitope specific interleukin-17 production by T cells @@ -93527,11 +111251,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ELISA - ELISA measuring epitope specific interleukin-18 production by T cells + ELISA measuring epitope specific interleukin-18 production by T cells + + An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|ELISA + ELISA measuring epitope specific interleukin-18 production by T cells @@ -93565,11 +111291,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunospot assay that detects interleukin-4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-4 production by T cells + ELISPOT assay measuring epitope specific interleukin-4 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-4 production by T cells @@ -93603,11 +111331,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunospot assay that detects tumor necrosis factor production by T cells. - IEDB - IEDB - TNFa release|ELISPOT - ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells + ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells + + An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells + IEDB + IEDB + TNFa release|ELISPOT + ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells @@ -93641,11 +111371,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-10 production by T cells + ELISPOT assay measuring epitope specific interleukin-10 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-10 production by T cells @@ -93679,11 +111411,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-13 production by T cells + ELISPOT assay measuring epitope specific interleukin-13 production by T cells + + An enzyme-linked immunospot assay that detects interleukin-13 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-13 production by T cells @@ -93717,11 +111451,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A flow cytometry assay that detects interferon-gamma production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ICS - intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells + intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells + + A flow cytometry assay that detects interferon-gamma production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ICS + intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells @@ -93755,11 +111491,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A flow cytometry assay that detects interleukin-2 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells + + A flow cytometry assay that detects interleukin-2 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells @@ -93793,11 +111531,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A flow cytometry assay that detects tumor necrosis factor production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|ICS - intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells + + A flow cytometry assay that detects tumor necrosis factor alpha production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|ICS + intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells @@ -93831,11 +111571,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A flow cytometry assay that detects interleukin-4 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells + + A flow cytometry assay that detects interleukin-4 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells @@ -93869,11 +111611,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A flow cytometry assay that detects interleukin-10 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells + + A flow cytometry assay that detects interleukin-10 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells @@ -93907,11 +111651,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A flow cytometry assay that detects interleukin-17 production by T cells. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ICS - intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells + intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells + + A flow cytometry assay that detects interleukin-17 production by T cells. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|ICS + intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells @@ -93961,11 +111707,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|multimer/tetramer - MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex + MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex + + A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|multimer/tetramer + MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex @@ -93976,26 +111724,50 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay. - IEDB - IEDB - proliferation|3H-thymidine - 3H-thymidine assay measuring epitope specific proliferation of T cells + 3H-thymidine assay measuring epitope specific proliferation of T cells + + A tritiated thymidine incorporation assay that detects T cell epitope specific proliferation in vitro. + IEDB + IEDB + proliferation|3H-thymidine + 3H-thymidine assay measuring epitope specific proliferation of T cells @@ -94006,26 +111778,50 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay. - IEDB - IEDB - proliferation|BrdU - BrdU assay measuring epitope specific proliferation of T cells + BrdU assay measuring epitope specific proliferation of T cells + + A BrdU incorporation assay that detects T cell epitope specific proliferation in vitro. + IEDB + IEDB + proliferation|BrdU + BrdU assay measuring epitope specific proliferation of T cells @@ -94044,7 +111840,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific T cell proliferation + epitope specific T cell proliferation A biological process where T cells proliferate resulting from the recognition of a T cell epitope. IEDB @@ -94069,7 +111865,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific GM-CSF release by T cells + epitope specific GM-CSF release by T cells A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope. IEDB @@ -94093,7 +111889,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IFN-g release by T cells + epitope specific IFN-g release by T cells A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope. IEDB @@ -94117,7 +111913,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-10 release by T cells + epitope specific IL-10 release by T cells A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope. IEDB @@ -94141,7 +111937,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-12 release by T cells + epitope specific IL-12 release by T cells A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope. IEDB @@ -94165,7 +111961,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-13 release by T cells + epitope specific IL-13 release by T cells A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope. IEDB @@ -94189,7 +111985,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-17 release by T cells + epitope specific IL-17 release by T cells A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope. IEDB @@ -94213,7 +112009,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-18 release by T cells + epitope specific IL-18 release by T cells A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope. IEDB @@ -94237,7 +112033,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-1b release by T cells + epitope specific IL-1b release by T cells A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope. IEDB @@ -94261,7 +112057,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-4 release by T cells + epitope specific IL-4 release by T cells A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope. IEDB @@ -94285,13 +112081,13 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - allergen - Birch pollen is an allergen + allergen + Birch pollen is an allergen - A material entity bearing the disposition to cause an allergic reaction - IEDB - IEDB - allergen + A material entity bearing the disposition to cause an allergic reaction + IEDB + IEDB + allergen @@ -94310,7 +112106,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-5 release by T cells + epitope specific IL-5 release by T cells A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope. IEDB @@ -94334,7 +112130,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific IL-6 release by T cells + epitope specific IL-6 release by T cells A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope. IEDB @@ -94358,7 +112154,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific killing by T cells + epitope specific killing by T cells A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell. IEDB @@ -94382,7 +112178,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - epitope specific TNF release by T cells + epitope specific TNF release by T cells A biological process where T cells produce TNF resulting from the recognition of a T cell epitope. IEDB @@ -94416,13 +112212,14 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - An IFN-g ELISPOT is an assay detecting ifn-gamma production + assay detecting IFN-gamma production + An IFN-g ELISPOT is an assay detecting ifn-gamma production - An assay that determines information about the production of the cytokine interferon gamma - Bjoern Peters - IFNg release - IEDB - assay detecting IFN-gamma production + An assay that determines information about the production of the cytokine interferon gamma + Bjoern Peters + IFNg release + IEDB + assay detecting IFN-gamma production @@ -94431,15 +112228,15 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - direct submission to IEDB - The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB. + direct submission to IEDB + The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB. The content of that report on the IEDB website is here: http://iedb.org/refId/1013357 - A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB) - PERSON: Bjoern Peters - IEDB - direct submission to IEDB + A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB) + PERSON: Bjoern Peters + IEDB + direct submission to IEDB @@ -94452,6 +112249,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 Many of today’s researchers prefer to use Formalin-Fixed Paraffin-Embedded samples of tissues for their IHC, histological or in-situ genomic analyses. Professionally fixed and embedded FFPE samples and the biomolecules they contain are reasonably stable at ambient temperatures. -based on https://lab-ally.com/histopathology-resources/ffpe-samples/ + A specimen that has been fixed in formalin and embedded in paraffin. MIABIS formalin-fixed paraffin-embeded specimen @@ -94468,28 +112266,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some uterine cervix - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - uterine cervix specimen + uterine cervix specimen + + A specimen that is derived from some uterine cervix + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + uterine cervix specimen @@ -94500,28 +112296,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some urethra - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - urethra specimen + urethra specimen + + A specimen that is derived from some urethra + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + urethra specimen @@ -94532,28 +112326,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some cervical mucus - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - cervical mucus specimen + cervical mucus specimen + + A specimen that is derived from some cervical mucus + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + cervical mucus specimen @@ -94564,28 +112356,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some throat - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - throat specimen + throat specimen + + A specimen that is derived from some throat + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + throat specimen @@ -94596,28 +112386,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some eye - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - eye specimen + eye specimen + + A specimen that is derived from some eye + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + eye specimen @@ -94628,28 +112416,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some respiratory system - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - respiratory system specimen + respiratory system specimen + + A specimen that is derived from some respiratory system + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + respiratory system specimen @@ -94660,28 +112446,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some upper respiratory tract - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - upper respiratory tract specimen + upper respiratory tract specimen + + A specimen that is derived from some upper respiratory tract + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + upper respiratory tract specimen @@ -94692,28 +112476,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some nasopharynx - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - nasopharynx specimen + nasopharynx specimen + + A specimen that is derived from some nasopharynx + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + nasopharynx specimen @@ -94724,28 +112506,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some semen - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - semen specimen + semen specimen + + A specimen that is derived from some semen + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + semen specimen @@ -94756,28 +112536,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some bodily fluid - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - bodily fluid specimen + bodily fluid specimen + + A specimen that is derived from some bodily fluid + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + bodily fluid specimen @@ -94788,28 +112566,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some chorionic villus - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - chorionic villus specimen + chorionic villus specimen + + A specimen that is derived from some chorionic villus + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + chorionic villus specimen @@ -94820,28 +112596,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some meconium - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - meconium specimen + meconium specimen + + A specimen that is derived from some meconium + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + meconium specimen @@ -94852,28 +112626,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some umbilical cord blood - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - umbilical cord blood specimen + umbilical cord blood specimen + + A specimen that is derived from some umbilical cord blood + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + umbilical cord blood specimen @@ -94884,28 +112656,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some arterial blood - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - arterial blood specimen + arterial blood specimen + + A specimen that is derived from some arterial blood + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + arterial blood specimen @@ -94916,28 +112686,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some venous blood - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - venous blood specimen + venous blood specimen + + A specimen that is derived from some venous blood + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + venous blood specimen @@ -94948,28 +112716,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - + + + + + + + + + - A specimen that is derived from some capillary blood - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - capillary blood specimen + capillary blood specimen + + A specimen that is derived from some capillary blood + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + capillary blood specimen @@ -94998,12 +112764,14 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A specimen that is derived from some erythrocytes - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - erythrocyte specimen + erythrocyte specimen + + A specimen that is derived from some erythrocytes + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + erythrocyte specimen @@ -95032,12 +112800,14 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A specimen that is derived from some reticulocytes - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - reticulocyte specimen + reticulocyte specimen + + A specimen that is derived from some reticulocytes + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + reticulocyte specimen @@ -95066,12 +112836,14 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A specimen that is derived from some leukocytes - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - Christian Stoeckert ORCID:0000-0002-5714-991X - Mark A. Miller ORCID:0000-0001-9076-6066 - leukocyte specimen + leukocyte specimen + + A specimen that is derived from some leukocytes + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + leukocyte specimen @@ -95108,11 +112880,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - carbon dioxide assay + carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + carbon dioxide assay @@ -95149,11 +112923,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium(1+) - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - sodium(1+) assay + sodium(1+) assay + + An analyte assay that measures the abundance of sodium(1+) + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + sodium(1+) assay @@ -95190,11 +112966,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - creatinine assay + creatinine assay + + An analyte assay that measures the abundance of creatinine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + creatinine assay @@ -95231,11 +113009,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium(1+) - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - potassium(1+) assay + potassium(1+) assay + + An analyte assay that measures the abundance of potassium(1+) + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + potassium(1+) assay @@ -95255,11 +113035,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of basophils - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - basophil count assay + basophil count assay + + A cytometry assay that measures the count of basophils + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + basophil count assay @@ -95279,11 +113061,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of neutrophils - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - neutrophil count assay + neutrophil count assay + + A cytometry assay that measures the count of neutrophils + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + neutrophil count assay @@ -95303,11 +113087,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of eosinophils - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - eosinophil count assay + eosinophil count assay + + A cytometry assay that measures the count of eosinophils + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + eosinophil count assay @@ -95327,11 +113113,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of lymphocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lymphocyte count assay + lymphocyte count assay + + A cytometry assay that measures the count of lymphocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lymphocyte count assay @@ -95351,11 +113139,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of monocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - monocyte count assay + monocyte count assay + + A cytometry assay that measures the count of monocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + monocyte count assay @@ -95392,11 +113182,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chloride assay + chloride assay + + An analyte assay that measures the abundance of chloride + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chloride assay @@ -95416,11 +113208,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of erythrocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - erythrocyte count assay + erythrocyte count assay + + A cytometry assay that measures the count of erythrocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + erythrocyte count assay @@ -95440,11 +113234,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of platelets - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - platelet count assay + platelet count assay + + A cytometry assay that measures the count of platelets + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + platelet count assay @@ -95464,11 +113260,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of leukocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - leukocyte count assay + leukocyte count assay + + A cytometry assay that measures the count of leukocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + leukocyte count assay @@ -95505,11 +113303,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hemoglobin assay + hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hemoglobin assay @@ -95546,11 +113346,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of phosphate ion - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - phosphate ion assay + phosphate ion assay + + An analyte assay that measures the abundance of phosphate ion + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + phosphate ion assay @@ -95587,11 +113389,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of alanine aminotransferase - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - alanine aminotransferase assay + alanine aminotransferase assay + + An analyte assay that measures the abundance of alanine aminotransferase + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + alanine aminotransferase assay @@ -95628,11 +113432,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of alkaline phosphatase (human) - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - alkaline phosphatase (human) assay + alkaline phosphatase (human) assay + + An analyte assay that measures the abundance of alkaline phosphatase (human) + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + alkaline phosphatase (human) assay @@ -95669,11 +113475,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bilirubin IXalpha - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bilirubin IXalpha assay + bilirubin IXalpha assay + + An analyte assay that measures the abundance of bilirubin IXalpha + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bilirubin IXalpha assay @@ -95710,11 +113518,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of aspartate aminotransferase (human) - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - aspartate aminotransferase (human) assay + aspartate aminotransferase (human) assay + + An analyte assay that measures the abundance of aspartate aminotransferase (human) + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + aspartate aminotransferase (human) assay @@ -95751,11 +113561,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - glucose assay + glucose assay + + An analyte assay that measures the abundance of glucose + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + glucose assay @@ -95792,11 +113604,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of magnesium cation - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - magnesium cation assay + magnesium cation assay + + An analyte assay that measures the abundance of magnesium cation + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + magnesium cation assay @@ -95833,11 +113647,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - albumin assay + albumin assay + + An analyte assay that measures the abundance of albumin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + albumin assay @@ -95874,11 +113690,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - protein assay + protein assay + + An analyte assay that measures the abundance of protein + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + protein assay @@ -95915,11 +113733,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium cation - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - calcium cation assay + calcium cation assay + + An analyte assay that measures the abundance of calcium cation + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + calcium cation assay @@ -95956,11 +113776,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatine kinase - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - creatine kinase assay + creatine kinase assay + + An analyte assay that measures the abundance of creatine kinase + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + creatine kinase assay @@ -95980,11 +113802,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of nucleate erythrocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - nucleate erythrocyte count assay + nucleate erythrocyte count assay + + A cytometry assay that measures the count of nucleate erythrocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + nucleate erythrocyte count assay @@ -96004,11 +113828,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of segmented neutrophil of bone marrows - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - segmented neutrophil of bone marrow count assay + segmented neutrophil of bone marrow count assay + + A cytometry assay that measures the count of segmented neutrophil of bone marrows + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + segmented neutrophil of bone marrow count assay @@ -96032,11 +113858,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures lactate dehydrogenase complex - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lactate dehydrogenase complex assay + lactate dehydrogenase complex assay + + An assay that measures lactate dehydrogenase complex + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lactate dehydrogenase complex assay @@ -96073,11 +113901,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of triglyceride - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - triglyceride assay + triglyceride assay + + An analyte assay that measures the abundance of triglyceride + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + triglyceride assay @@ -96114,11 +113944,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of high-density lipoprotein cholesterol - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - high-density lipoprotein cholesterol assay + high-density lipoprotein cholesterol assay + + An analyte assay that measures the abundance of high-density lipoprotein cholesterol + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + high-density lipoprotein cholesterol assay @@ -96155,11 +113987,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of cholesterol - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cholesterol assay + cholesterol assay + + An analyte assay that measures the abundance of cholesterol + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cholesterol assay @@ -96196,11 +114030,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of low-density lipoprotein cholesterol - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - low-density lipoprotein cholesterol assay + low-density lipoprotein cholesterol assay + + An analyte assay that measures the abundance of low-density lipoprotein cholesterol + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + low-density lipoprotein cholesterol assay @@ -96237,11 +114073,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of thyroid stimulating hormone - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - thyroid stimulating hormone assay + thyroid stimulating hormone assay + + An analyte assay that measures the abundance of thyroid stimulating hormone + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + thyroid stimulating hormone assay @@ -96278,11 +114116,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of prostate-specific antigen - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - prostate-specific antigen assay + prostate-specific antigen assay + + An analyte assay that measures the abundance of prostate-specific antigen + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + prostate-specific antigen assay @@ -96319,11 +114159,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of thyroxine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - thyroxine assay + thyroxine assay + + An analyte assay that measures the abundance of thyroxine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + thyroxine assay @@ -96360,11 +114202,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of elemental oxygen - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - elemental oxygen assay + elemental oxygen assay + + An analyte assay that measures the abundance of elemental oxygen + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + elemental oxygen assay @@ -96401,11 +114245,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of folic acids - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - folic acids assay + folic acids assay + + An analyte assay that measures the abundance of folic acids + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + folic acids assay @@ -96425,11 +114271,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of reticulocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - reticulocyte count assay + reticulocyte count assay + + A cytometry assay that measures the count of reticulocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + reticulocyte count assay @@ -96453,11 +114301,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures osmolality - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - osmolality assay + osmolality assay + + An assay that measures osmolality + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + osmolality assay @@ -96494,11 +114344,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of methemoglobin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - methemoglobin assay + methemoglobin assay + + An analyte assay that measures the abundance of methemoglobin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + methemoglobin assay @@ -96522,11 +114374,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures cytosolic creatine kinase complex, MB-type - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cytosolic creatine kinase complex, MB-type assay + cytosolic creatine kinase complex, MB-type assay + + An assay that measures cytosolic creatine kinase complex, MB-type + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cytosolic creatine kinase complex, MB-type assay @@ -96550,11 +114404,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures rac-lactic acid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - rac-lactic acid assay + rac-lactic acid assay + + An assay that measures rac-lactic acid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + rac-lactic acid assay @@ -96591,11 +114447,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hydrogencarbonate - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hydrogencarbonate assay + hydrogencarbonate assay + + An analyte assay that measures the abundance of hydrogencarbonate + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hydrogencarbonate assay @@ -96632,11 +114490,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of vancomycin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - vancomycin assay + vancomycin assay + + An analyte assay that measures the abundance of vancomycin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + vancomycin assay @@ -96673,11 +114533,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of tobramycin - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - tobramycin assay + tobramycin assay + + An analyte assay that measures the abundance of tobramycin + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + tobramycin assay @@ -96714,11 +114576,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of 3,3',5'-triiodothyronine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - 3,3',5'-triiodothyronine assay + 3,3',5'-triiodothyronine assay + + An analyte assay that measures the abundance of 3,3',5'-triiodothyronine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + 3,3',5'-triiodothyronine assay @@ -96755,11 +114619,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of C-reactive protein - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - C-reactive protein assay + C-reactive protein assay + + An analyte assay that measures the abundance of C-reactive protein + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + C-reactive protein assay @@ -96779,11 +114645,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of megakaryocytes - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - megakaryocyte count assay + megakaryocyte count assay + + A cytometry assay that measures the count of megakaryocytes + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + megakaryocyte count assay @@ -96803,11 +114671,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of mesothelial cells - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - mesothelial cell count assay + mesothelial cell count assay + + A cytometry assay that measures the count of mesothelial cells + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + mesothelial cell count assay @@ -96827,11 +114697,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of macrophages - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - macrophage count assay + macrophage count assay + + A cytometry assay that measures the count of macrophages + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + macrophage count assay @@ -96868,11 +114740,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of 3-hydroxybutyric acid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - 3-hydroxybutyric acid assay + 3-hydroxybutyric acid assay + + An analyte assay that measures the abundance of 3-hydroxybutyric acid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + 3-hydroxybutyric acid assay @@ -96939,11 +114813,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - panel5 venous blood carbon dioxide assay + panel5 venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + panel5 venous blood carbon dioxide assay @@ -97010,11 +114886,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - panel5 venous blood sodium assay + panel5 venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + panel5 venous blood sodium assay @@ -97081,11 +114959,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - panel5 venous blood creatinine assay + panel5 venous blood creatinine assay + + An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + panel5 venous blood creatinine assay @@ -97152,11 +115032,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - panel5 venous blood potassium assay + panel5 venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + panel5 venous blood potassium assay @@ -97210,11 +115092,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - automated differential venous blood basophil count assay + automated differential venous blood basophil count assay + + A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + automated differential venous blood basophil count assay @@ -97268,11 +115152,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - automated differential venous blood neutrophil count assay + automated differential venous blood neutrophil count assay + + A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + automated differential venous blood neutrophil count assay @@ -97326,11 +115212,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - automated differential venous blood eosinophil count assay + automated differential venous blood eosinophil count assay + + A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + automated differential venous blood eosinophil count assay @@ -97384,11 +115272,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - automated differential venous blood lymphocyte count assay + automated differential venous blood lymphocyte count assay + + A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + automated differential venous blood lymphocyte count assay @@ -97442,11 +115332,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - automated differential venous blood monocyte count assay + automated differential venous blood monocyte count assay + + A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + automated differential venous blood monocyte count assay @@ -97513,11 +115405,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood chloride assay + venous blood chloride assay + + An analyte assay that measures the abundance of chloride in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood chloride assay @@ -97571,11 +115465,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with automated differential venous blood RBC count assay + CBC with automated differential venous blood RBC count assay + + A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with automated differential venous blood RBC count assay @@ -97629,11 +115525,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with automated differential venous blood platelet count assay + CBC with automated differential venous blood platelet count assay + + A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with automated differential venous blood platelet count assay @@ -97687,11 +115585,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with automated differential venous blood WBC count assay + CBC with automated differential venous blood WBC count assay + + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with automated differential venous blood WBC count assay @@ -97745,11 +115645,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with automated differential venous blood hematocrit assay + CBC with automated differential venous blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with automated differential venous blood hematocrit assay @@ -97816,11 +115718,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with automated differential venous blood hemoglobin assay + CBC with automated differential venous blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with automated differential venous blood hemoglobin assay @@ -97887,11 +115791,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of phosphate in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood phosphate assay + venous blood phosphate assay + + An analyte assay that measures the abundance of phosphate in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood phosphate assay @@ -97958,11 +115864,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver injury venous blood alanine aminotransferase assay + liver injury venous blood alanine aminotransferase assay + + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver injury venous blood alanine aminotransferase assay @@ -98029,11 +115937,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver injury venous blood human alkaline phosphatase assay + liver injury venous blood human alkaline phosphatase assay + + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver injury venous blood human alkaline phosphatase assay @@ -98100,11 +116010,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver injury venous blood bilirubin assay + liver injury venous blood bilirubin assay + + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver injury venous blood bilirubin assay @@ -98171,11 +116083,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver injury venous blood human aspartate aminotransferase assay + liver injury venous blood human aspartate aminotransferase assay + + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver injury venous blood human aspartate aminotransferase assay @@ -98242,11 +116156,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood glucose assay + venous blood glucose assay + + An analyte assay that measures the abundance of glucose in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood glucose assay @@ -98313,11 +116229,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of magnesium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood magnesium assay + venous blood magnesium assay + + An analyte assay that measures the abundance of magnesium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood magnesium assay @@ -98371,11 +116289,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC venous blood RBC count assay + CBC venous blood RBC count assay + + A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC venous blood RBC count assay @@ -98429,11 +116349,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC venous blood WBC count assay + CBC venous blood WBC count assay + + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC venous blood WBC count assay @@ -98487,11 +116409,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC venous blood hematocrit assay + CBC venous blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC venous blood hematocrit assay @@ -98545,11 +116469,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of platelets in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC venous blood platelet count assay + CBC venous blood platelet count assay + + A cytometry assay that measures the count of platelets in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC venous blood platelet count assay @@ -98616,11 +116542,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC venous blood hemoglobin assay + CBC venous blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC venous blood hemoglobin assay @@ -98674,11 +116602,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - corrected venous blood leukocyte count assay + corrected venous blood leukocyte count assay + + A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + corrected venous blood leukocyte count assay @@ -98745,11 +116675,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver evaluation venous blood bilirubin assay + liver evaluation venous blood bilirubin assay + + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver evaluation venous blood bilirubin assay @@ -98816,11 +116748,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver evaluation venous blood globulin assay + liver evaluation venous blood globulin assay + + An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver evaluation venous blood globulin assay @@ -98887,11 +116821,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver evaluation venous blood albumin assay + liver evaluation venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver evaluation venous blood albumin assay @@ -98958,11 +116894,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver evaluation venous blood human aspartate aminotransferase assay + liver evaluation venous blood human aspartate aminotransferase assay + + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver evaluation venous blood human aspartate aminotransferase assay @@ -99029,11 +116967,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver evaluation venous blood alanine aminotransferase assay + liver evaluation venous blood alanine aminotransferase assay + + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver evaluation venous blood alanine aminotransferase assay @@ -99100,11 +117040,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver evaluation venous blood human alkaline phosphatase assay + liver evaluation venous blood human alkaline phosphatase assay + + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver evaluation venous blood human alkaline phosphatase assay @@ -99171,11 +117113,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver evaluation venous blood protein assay + liver evaluation venous blood protein assay + + An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver evaluation venous blood protein assay @@ -99242,11 +117186,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - basic metabolic panel venous blood chloride assay + basic metabolic panel venous blood chloride assay + + An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + basic metabolic panel venous blood chloride assay @@ -99313,11 +117259,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - basic metabolic panel venous blood potassium assay + basic metabolic panel venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + basic metabolic panel venous blood potassium assay @@ -99384,11 +117332,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - basic metabolic panel venous blood sodium assay + basic metabolic panel venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + basic metabolic panel venous blood sodium assay @@ -99455,11 +117405,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - basic metabolic panel venous blood creatinine assay + basic metabolic panel venous blood creatinine assay + + An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + basic metabolic panel venous blood creatinine assay @@ -99526,11 +117478,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - basic metabolic panel venous blood glucose assay + basic metabolic panel venous blood glucose assay + + An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + basic metabolic panel venous blood glucose assay @@ -99597,11 +117551,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - basic metabolic panel venous blood calcium assay + basic metabolic panel venous blood calcium assay + + An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + basic metabolic panel venous blood calcium assay @@ -99668,11 +117624,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - basic metabolic panel venous blood carbon dioxide assay + basic metabolic panel venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + basic metabolic panel venous blood carbon dioxide assay @@ -99739,11 +117697,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatine kinase in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood creatine kinase assay + venous blood creatine kinase assay + + An analyte assay that measures the abundance of creatine kinase in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood creatine kinase assay @@ -99810,11 +117770,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood calcium assay + venous blood calcium assay + + An analyte assay that measures the abundance of calcium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood calcium assay @@ -99868,11 +117830,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures ferritin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood ferritin assay + venous blood ferritin assay + + An assay that measures ferritin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood ferritin assay @@ -99939,11 +117903,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - total venous blood calcium assay + total venous blood calcium assay + + An analyte assay that measures the abundance of calcium in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total venous blood calcium assay @@ -100010,11 +117976,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of iron in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood iron assay + venous blood iron assay + + An analyte assay that measures the abundance of iron in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood iron assay @@ -100068,11 +118036,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood band neutrophil count assay + CBC with manual differential venous blood band neutrophil count assay + + A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood band neutrophil count assay @@ -100126,11 +118096,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood WBC count assay + CBC with manual differential venous blood WBC count assay + + A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood WBC count assay @@ -100184,11 +118156,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood eosinophil count assay + CBC with manual differential venous blood eosinophil count assay + + A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood eosinophil count assay @@ -100242,11 +118216,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood lymphocyte count assay + CBC with manual differential venous blood lymphocyte count assay + + A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood lymphocyte count assay @@ -100300,11 +118276,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood nucleated RBC count assay + CBC with manual differential venous blood nucleated RBC count assay + + A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood nucleated RBC count assay @@ -100358,11 +118336,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood monocyte count assay + CBC with manual differential venous blood monocyte count assay + + A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood monocyte count assay @@ -100416,11 +118396,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood segmented neutrophil count assay + CBC with manual differential venous blood segmented neutrophil count assay + + A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood segmented neutrophil count assay @@ -100474,11 +118456,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood basophil count assay + CBC with manual differential venous blood basophil count assay + + A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood basophil count assay @@ -100545,11 +118529,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood albumin assay + venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood albumin assay @@ -100616,11 +118602,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cardiac enzymes venous blood creatine kinase assay + cardiac enzymes venous blood creatine kinase assay + + An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cardiac enzymes venous blood creatine kinase assay @@ -100687,11 +118675,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of haptoglobin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood haptoglobin assay + venous blood haptoglobin assay + + An analyte assay that measures the abundance of haptoglobin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood haptoglobin assay @@ -100745,11 +118735,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures lactate dehydrogenase in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood lactate dehydrogenase assay + venous blood lactate dehydrogenase assay + + An assay that measures lactate dehydrogenase in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood lactate dehydrogenase assay @@ -100816,11 +118808,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of prealbunin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood prealbunin assay + venous blood prealbunin assay + + An analyte assay that measures the abundance of prealbunin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood prealbunin assay @@ -100887,11 +118881,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel venous blood triglyceride assay + lipid panel venous blood triglyceride assay + + An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lipid panel venous blood triglyceride assay @@ -100958,11 +118954,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel venous blood high density lipoprotein assay + lipid panel venous blood high density lipoprotein assay + + An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lipid panel venous blood high density lipoprotein assay @@ -101029,11 +119027,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel venous blood cholesterol assay + lipid panel venous blood cholesterol assay + + An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lipid panel venous blood cholesterol assay @@ -101100,11 +119100,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel venous blood low density lipoprotein assay + lipid panel venous blood low density lipoprotein assay + + An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lipid panel venous blood low density lipoprotein assay @@ -101158,11 +119160,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures hemoglobin A1c in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood hemoglobin A1c assay + venous blood hemoglobin A1c assay + + An assay that measures hemoglobin A1c in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood hemoglobin A1c assay @@ -101229,11 +119233,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of uric acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood uric acid assay + venous blood uric acid assay + + An analyte assay that measures the abundance of uric acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood uric acid assay @@ -101300,11 +119306,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - total venous blood protein assay + total venous blood protein assay + + An analyte assay that measures the abundance of protein in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total venous blood protein assay @@ -101371,11 +119379,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood thyroid stimulating hormone assay + venous blood thyroid stimulating hormone assay + + An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood thyroid stimulating hormone assay @@ -101442,11 +119452,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of prostate specific antigen in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood prostate specific antigen assay + venous blood prostate specific antigen assay + + An analyte assay that measures the abundance of prostate specific antigen in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood prostate specific antigen assay @@ -101500,11 +119512,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures volume in urine as part of a 24 hour total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - 24 hour total urine volume assay + 24 hour total urine volume assay + + An assay that measures volume in urine as part of a 24 hour total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + 24 hour total urine volume assay @@ -101571,11 +119585,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - T4 uptake venous blood T4 assay + T4 uptake venous blood T4 assay + + An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + T4 uptake venous blood T4 assay @@ -101642,11 +119658,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - arterial blood glucose assay + arterial blood glucose assay + + An analyte assay that measures the abundance of glucose in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + arterial blood glucose assay @@ -101700,11 +119718,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood cell count assay + CBC with manual differential venous blood cell count assay + + A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood cell count assay @@ -101771,11 +119791,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hemoglobin oxygen saturation arterial blood oxygen assay + hemoglobin oxygen saturation arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hemoglobin oxygen saturation arterial blood oxygen assay @@ -101842,11 +119864,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hemoglobin oxygen saturation arterial blood hemoglobin assay + hemoglobin oxygen saturation arterial blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hemoglobin oxygen saturation arterial blood hemoglobin assay @@ -101913,11 +119937,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - inpatient profile venous blood sodium assay + inpatient profile venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + inpatient profile venous blood sodium assay @@ -101984,11 +120010,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - inpatient profile venous blood creatinine assay + inpatient profile venous blood creatinine assay + + An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + inpatient profile venous blood creatinine assay @@ -102055,11 +120083,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - inpatient profile venous blood potassium assay + inpatient profile venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + inpatient profile venous blood potassium assay @@ -102126,11 +120156,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - inpatient profile venous blood carbon dioxide assay + inpatient profile venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + inpatient profile venous blood carbon dioxide assay @@ -102197,11 +120229,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of folic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood folic acid assay + venous blood folic acid assay + + An analyte assay that measures the abundance of folic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood folic acid assay @@ -102255,11 +120289,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - count venous blood reticulocyte count assay + count venous blood reticulocyte count assay + + A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + count venous blood reticulocyte count assay @@ -102326,11 +120362,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood potassium assay + venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood potassium assay @@ -102397,11 +120435,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood carbon dioxide assay + venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood carbon dioxide assay @@ -102468,11 +120508,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of transferrin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood transferrin assay + venous blood transferrin assay + + An analyte assay that measures the abundance of transferrin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood transferrin assay @@ -102539,11 +120581,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood sodium assay + venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood sodium assay @@ -102610,11 +120654,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - random electrolytes urine sodium assay + random electrolytes urine sodium assay + + An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + random electrolytes urine sodium assay @@ -102681,11 +120727,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - random electrolytes urine potassium assay + random electrolytes urine potassium assay + + An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + random electrolytes urine potassium assay @@ -102752,11 +120800,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in urine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - urine creatinine assay + urine creatinine assay + + An analyte assay that measures the abundance of creatinine in urine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + urine creatinine assay @@ -102810,11 +120860,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures osmolality in urine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - urine osmolality assay + urine osmolality assay + + An assay that measures osmolality in urine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + urine osmolality assay @@ -102881,11 +120933,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cooximitery arterial blood oxygen assay + cooximitery arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cooximitery arterial blood oxygen assay @@ -102952,11 +121006,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cooximitery arterial blood hemoglobin assay + cooximitery arterial blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cooximitery arterial blood hemoglobin assay @@ -103023,11 +121079,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cooximitery arterial blood methemoglobin assay + cooximitery arterial blood methemoglobin assay + + An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cooximitery arterial blood methemoglobin assay @@ -103094,11 +121152,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - electrolytes urine sodium assay + electrolytes urine sodium assay + + An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + electrolytes urine sodium assay @@ -103165,11 +121225,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - electrolytes urine potassium assay + electrolytes urine potassium assay + + An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + electrolytes urine potassium assay @@ -103223,11 +121285,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - Biosite cardiac panel arterial blood creatine kinase MB assay + Biosite cardiac panel arterial blood creatine kinase MB assay + + An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + Biosite cardiac panel arterial blood creatine kinase MB assay @@ -103281,11 +121345,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures fibrinogen in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood fibrinogen assay + venous blood fibrinogen assay + + An assay that measures fibrinogen in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood fibrinogen assay @@ -103352,11 +121418,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood carbon dioxide assay + comprehensive metabolic panel venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood carbon dioxide assay @@ -103423,11 +121491,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood calcium assay + comprehensive metabolic panel venous blood calcium assay + + An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood calcium assay @@ -103494,11 +121564,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood potassium assay + comprehensive metabolic panel venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood potassium assay @@ -103565,11 +121637,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood sodium assay + comprehensive metabolic panel venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood sodium assay @@ -103636,11 +121710,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood glucose assay + comprehensive metabolic panel venous blood glucose assay + + An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood glucose assay @@ -103707,11 +121783,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood albumin assay + comprehensive metabolic panel venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood albumin assay @@ -103778,11 +121856,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood human alkaline phosphatase assay + comprehensive metabolic panel venous blood human alkaline phosphatase assay + + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood human alkaline phosphatase assay @@ -103849,11 +121929,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood bilirubin assay + comprehensive metabolic panel venous blood bilirubin assay + + An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood bilirubin assay @@ -103920,11 +122002,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood chloride assay + comprehensive metabolic panel venous blood chloride assay + + An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood chloride assay @@ -103991,11 +122075,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood human aspartate aminotransferase assay + comprehensive metabolic panel venous blood human aspartate aminotransferase assay + + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood human aspartate aminotransferase assay @@ -104062,11 +122148,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood protein assay + comprehensive metabolic panel venous blood protein assay + + An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood protein assay @@ -104133,11 +122221,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood creatinine assay + comprehensive metabolic panel venous blood creatinine assay + + An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood creatinine assay @@ -104204,11 +122294,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - comprehensive metabolic panel venous blood alanine aminotransferase assay + comprehensive metabolic panel venous blood alanine aminotransferase assay + + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + comprehensive metabolic panel venous blood alanine aminotransferase assay @@ -104262,11 +122354,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures LDH in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood LDH assay + venous blood LDH assay + + An assay that measures LDH in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood LDH assay @@ -104320,11 +122414,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures creatine kinase MB in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood creatine kinase MB assay + venous blood creatine kinase MB assay + + An assay that measures creatine kinase MB in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood creatine kinase MB assay @@ -104378,11 +122474,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures lactic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood lactic acid assay + venous blood lactic acid assay + + An assay that measures lactic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood lactic acid assay @@ -104436,11 +122534,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood hematocrit assay + venous blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood hematocrit assay @@ -104507,11 +122607,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood creatinine assay + venous blood creatinine assay + + An analyte assay that measures the abundance of creatinine in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood creatinine assay @@ -104578,11 +122680,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - blood gas venous blood oxygen assay + blood gas venous blood oxygen assay + + An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + blood gas venous blood oxygen assay @@ -104649,11 +122753,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ionized venous blood ionized calcium assay + ionized venous blood ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ionized venous blood ionized calcium assay @@ -104720,11 +122826,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - blood gas venous blood carbon dioxide assay + blood gas venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + blood gas venous blood carbon dioxide assay @@ -104791,11 +122899,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - blood gas venous blood bicarbonate assay + blood gas venous blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + blood gas venous blood bicarbonate assay @@ -104862,11 +122972,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - arterial blood creatinine assay + arterial blood creatinine assay + + An analyte assay that measures the abundance of creatinine in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + arterial blood creatinine assay @@ -104933,11 +123045,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of tacrolimus in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood tacrolimus assay + venous blood tacrolimus assay + + An analyte assay that measures the abundance of tacrolimus in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood tacrolimus assay @@ -105004,11 +123118,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - random venous blood vancomycin assay + random venous blood vancomycin assay + + An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + random venous blood vancomycin assay @@ -105075,11 +123191,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of mycophenolic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood mycophenolic acid assay + venous blood mycophenolic acid assay + + An analyte assay that measures the abundance of mycophenolic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood mycophenolic acid assay @@ -105146,11 +123264,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - non-vented blood gas arterial blood carbon dioxide assay + non-vented blood gas arterial blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + non-vented blood gas arterial blood carbon dioxide assay @@ -105217,11 +123337,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - non-vented blood gas arterial blood oxygen assay + non-vented blood gas arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + non-vented blood gas arterial blood oxygen assay @@ -105288,11 +123410,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - non-vented blood gas arterial blood bicarbonate assay + non-vented blood gas arterial blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + non-vented blood gas arterial blood bicarbonate assay @@ -105346,11 +123470,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures IgG in venous blood as part of a quantitative order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - quantitative venous blood IgG assay + quantitative venous blood IgG assay + + An assay that measures IgG in venous blood as part of a quantitative order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + quantitative venous blood IgG assay @@ -105404,11 +123530,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures IgM in venous blood as part of a quantitative order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - quantitative venous blood IgM assay + quantitative venous blood IgM assay + + An assay that measures IgM in venous blood as part of a quantitative order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + quantitative venous blood IgM assay @@ -105462,11 +123590,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures IgA in venous blood as part of a quantitative order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - quantitative venous blood IgA assay + quantitative venous blood IgA assay + + An assay that measures IgA in venous blood as part of a quantitative order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + quantitative venous blood IgA assay @@ -105533,11 +123663,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - arterial blood sodium assay + arterial blood sodium assay + + An analyte assay that measures the abundance of sodium in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + arterial blood sodium assay @@ -105604,11 +123736,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - arterial blood potassium assay + arterial blood potassium assay + + An analyte assay that measures the abundance of potassium in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + arterial blood potassium assay @@ -105675,11 +123809,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ionized arterial blood calcium assay + ionized arterial blood calcium assay + + An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ionized arterial blood calcium assay @@ -105746,11 +123882,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - vented blood gas arterial blood bicarbonate assay + vented blood gas arterial blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + vented blood gas arterial blood bicarbonate assay @@ -105817,11 +123955,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - vented blood gas arterial blood oxygen assay + vented blood gas arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + vented blood gas arterial blood oxygen assay @@ -105888,11 +124028,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - vented blood gas arterial blood carbon dioxide assay + vented blood gas arterial blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + vented blood gas arterial blood carbon dioxide assay @@ -105946,11 +124088,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - arterial blood hematocrit assay + arterial blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + arterial blood hematocrit assay @@ -106017,11 +124161,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - arterial blood chloride assay + arterial blood chloride assay + + An analyte assay that measures the abundance of chloride in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + arterial blood chloride assay @@ -106088,11 +124234,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - arterial blood hemoglobin assay + arterial blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + arterial blood hemoglobin assay @@ -106146,11 +124294,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood hematocrit assay + GEM premier blood gas venous blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood hematocrit assay @@ -106217,11 +124367,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood ionized calcium assay + GEM premier blood gas venous blood ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood ionized calcium assay @@ -106288,11 +124440,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood potassium assay + GEM premier blood gas venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood potassium assay @@ -106359,11 +124513,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood oxygen assay + GEM premier blood gas venous blood oxygen assay + + An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood oxygen assay @@ -106430,11 +124586,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood hemoglobin assay + GEM premier blood gas venous blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood hemoglobin assay @@ -106501,11 +124659,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood bicarbonate assay + GEM premier blood gas venous blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood bicarbonate assay @@ -106572,11 +124732,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood glucose assay + GEM premier blood gas venous blood glucose assay + + An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood glucose assay @@ -106643,11 +124805,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood sodium assay + GEM premier blood gas venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood sodium assay @@ -106701,11 +124865,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood lactic acid assay + GEM premier blood gas venous blood lactic acid assay + + An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood lactic acid assay @@ -106772,11 +124938,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM premier blood gas venous blood carbon dioxide assay + GEM premier blood gas venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM premier blood gas venous blood carbon dioxide assay @@ -106843,11 +125011,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - trough venous blood tobramycin assay + trough venous blood tobramycin assay + + An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + trough venous blood tobramycin assay @@ -106914,11 +125084,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - random venous blood tobramycin assay + random venous blood tobramycin assay + + An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + random venous blood tobramycin assay @@ -106972,11 +125144,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood metamyelocyte count assay + CBC with manual differential venous blood metamyelocyte count assay + + A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood metamyelocyte count assay @@ -107030,11 +125204,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures lactic acid in arterial blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - arterial blood lactic acid assay + arterial blood lactic acid assay + + An assay that measures lactic acid in arterial blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + arterial blood lactic acid assay @@ -107101,11 +125277,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood 25-hydroxyvitamin D2 assay + venous blood 25-hydroxyvitamin D2 assay + + An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood 25-hydroxyvitamin D2 assay @@ -107172,11 +125350,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of digoxin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood digoxin assay + venous blood digoxin assay + + An analyte assay that measures the abundance of digoxin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood digoxin assay @@ -107243,11 +125423,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in urine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - urine protein assay + urine protein assay + + An analyte assay that measures the abundance of protein in urine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + urine protein assay @@ -107314,11 +125496,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of tobramycin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood tobramycin assay + venous blood tobramycin assay + + An analyte assay that measures the abundance of tobramycin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood tobramycin assay @@ -107372,11 +125556,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood myelocyte count assay + CBC with manual differential venous blood myelocyte count assay + + A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood myelocyte count assay @@ -107443,11 +125629,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - SPEP protein electrophoresis venous blood beta-globin assay + SPEP protein electrophoresis venous blood beta-globin assay + + An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + SPEP protein electrophoresis venous blood beta-globin assay @@ -107514,11 +125702,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - SPEP protein electrophoresis venous blood albumin assay + SPEP protein electrophoresis venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + SPEP protein electrophoresis venous blood albumin assay @@ -107585,11 +125775,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - SPEP protein electrophoresis venous blood protein assay + SPEP protein electrophoresis venous blood protein assay + + An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + SPEP protein electrophoresis venous blood protein assay @@ -107656,11 +125848,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - trough venous blood vancomycin assay + trough venous blood vancomycin assay + + An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + trough venous blood vancomycin assay @@ -107727,11 +125921,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hepatic panel venous blood protein assay + hepatic panel venous blood protein assay + + An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hepatic panel venous blood protein assay @@ -107798,11 +125994,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hepatic panel venous blood bilirubin assay + hepatic panel venous blood bilirubin assay + + An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hepatic panel venous blood bilirubin assay @@ -107869,11 +126067,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hepatic panel venous blood alanine aminotransferase assay + hepatic panel venous blood alanine aminotransferase assay + + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hepatic panel venous blood alanine aminotransferase assay @@ -107940,11 +126140,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hepatic panel venous blood human aspartate aminotransferase assay + hepatic panel venous blood human aspartate aminotransferase assay + + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hepatic panel venous blood human aspartate aminotransferase assay @@ -108011,11 +126213,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hepatic panel venous blood albumin assay + hepatic panel venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hepatic panel venous blood albumin assay @@ -108082,11 +126286,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hepatic panel venous blood human alkaline phosphatase assay + hepatic panel venous blood human alkaline phosphatase assay + + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hepatic panel venous blood human alkaline phosphatase assay @@ -108140,11 +126346,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures glomerular filtration in venous blood as part of a estimated order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - estimated venous blood glomerular filtration assay + estimated venous blood glomerular filtration assay + + An assay that measures glomerular filtration in venous blood as part of a estimated order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + estimated venous blood glomerular filtration assay @@ -108211,11 +126419,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - DT60 venous blood creatinine assay + DT60 venous blood creatinine assay + + An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + DT60 venous blood creatinine assay @@ -108282,11 +126492,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - fasting venous blood glucose assay + fasting venous blood glucose assay + + An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + fasting venous blood glucose assay @@ -108353,11 +126565,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of amikacin in venous blood as part of a random order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - random venous blood amikacin assay + random venous blood amikacin assay + + An analyte assay that measures the abundance of amikacin in venous blood as part of a random order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + random venous blood amikacin assay @@ -108424,11 +126638,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ammonia in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood ammonia assay + venous blood ammonia assay + + An analyte assay that measures the abundance of ammonia in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood ammonia assay @@ -108495,11 +126711,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of GGT in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood GGT assay + venous blood GGT assay + + An analyte assay that measures the abundance of GGT in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood GGT assay @@ -108566,11 +126784,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood phosphate assay + chem11 venous blood phosphate assay + + An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood phosphate assay @@ -108637,11 +126857,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood potassium assay + chem11 venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood potassium assay @@ -108708,11 +126930,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood calcium assay + chem11 venous blood calcium assay + + An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood calcium assay @@ -108779,11 +127003,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood glucose assay + chem11 venous blood glucose assay + + An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood glucose assay @@ -108850,11 +127076,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood carbon dioxide assay + chem11 venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood carbon dioxide assay @@ -108921,11 +127149,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood albumin assay + chem11 venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood albumin assay @@ -108992,11 +127222,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood sodium assay + chem11 venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood sodium assay @@ -109063,11 +127295,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood magnesium assay + chem11 venous blood magnesium assay + + An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood magnesium assay @@ -109134,11 +127368,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood creatinine assay + chem11 venous blood creatinine assay + + An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood creatinine assay @@ -109205,11 +127441,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem11 venous blood chloride assay + chem11 venous blood chloride assay + + An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem11 venous blood chloride assay @@ -109263,11 +127501,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures IgE in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - total venous blood IgE assay + total venous blood IgE assay + + An assay that measures IgE in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total venous blood IgE assay @@ -109334,11 +127574,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood human aspartate aminotransferase assay + chem16 venous blood human aspartate aminotransferase assay + + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood human aspartate aminotransferase assay @@ -109405,11 +127647,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood creatinine assay + chem16 venous blood creatinine assay + + An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood creatinine assay @@ -109476,11 +127720,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood magnesium assay + chem16 venous blood magnesium assay + + An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood magnesium assay @@ -109547,11 +127793,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood carbon dioxide assay + chem16 venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood carbon dioxide assay @@ -109618,11 +127866,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood glucose assay + chem16 venous blood glucose assay + + An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood glucose assay @@ -109689,11 +127939,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood calcium assay + chem16 venous blood calcium assay + + An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood calcium assay @@ -109760,11 +128012,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood triglyceride assay + chem16 venous blood triglyceride assay + + An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood triglyceride assay @@ -109831,11 +128085,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood sodium assay + chem16 venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood sodium assay @@ -109902,11 +128158,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood phosphate assay + chem16 venous blood phosphate assay + + An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood phosphate assay @@ -109973,11 +128231,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood human alkaline phosphatase assay + chem16 venous blood human alkaline phosphatase assay + + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood human alkaline phosphatase assay @@ -110044,11 +128304,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood albumin assay + chem16 venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood albumin assay @@ -110115,11 +128377,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood bilirubin assay + chem16 venous blood bilirubin assay + + An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood bilirubin assay @@ -110186,11 +128450,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood chloride assay + chem16 venous blood chloride assay + + An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood chloride assay @@ -110257,11 +128523,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood alanine aminotransferase assay + chem16 venous blood alanine aminotransferase assay + + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood alanine aminotransferase assay @@ -110328,11 +128596,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - chem16 venous blood potassium assay + chem16 venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + chem16 venous blood potassium assay @@ -110399,11 +128669,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - POC chem8 arterial blood glucose assay + POC chem8 arterial blood glucose assay + + An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + POC chem8 arterial blood glucose assay @@ -110470,11 +128742,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - POC chem8 arterial blood ionized calcium assay + POC chem8 arterial blood ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + POC chem8 arterial blood ionized calcium assay @@ -110541,11 +128815,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - POC chem8 arterial blood potassium assay + POC chem8 arterial blood potassium assay + + An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + POC chem8 arterial blood potassium assay @@ -110612,11 +128888,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - POC chem8 arterial blood sodium assay + POC chem8 arterial blood sodium assay + + An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + POC chem8 arterial blood sodium assay @@ -110683,11 +128961,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - POC chem8 arterial blood creatinine assay + POC chem8 arterial blood creatinine assay + + An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + POC chem8 arterial blood creatinine assay @@ -110741,11 +129021,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - POC chem8 arterial blood hematocrit assay + POC chem8 arterial blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + POC chem8 arterial blood hematocrit assay @@ -110812,11 +129094,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - POC chem8 arterial blood chloride assay + POC chem8 arterial blood chloride assay + + An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + POC chem8 arterial blood chloride assay @@ -110883,11 +129167,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - peak venous blood tobramycin assay + peak venous blood tobramycin assay + + An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + peak venous blood tobramycin assay @@ -110954,11 +129240,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - 24 hour urine creatinine assay + 24 hour urine creatinine assay + + An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + 24 hour urine creatinine assay @@ -111025,11 +129313,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of PTH in venous blood as part of a intact order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - intact venous blood PTH assay + intact venous blood PTH assay + + An analyte assay that measures the abundance of PTH in venous blood as part of a intact order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + intact venous blood PTH assay @@ -111096,11 +129386,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of PSA in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - total venous blood PSA assay + total venous blood PSA assay + + An analyte assay that measures the abundance of PSA in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total venous blood PSA assay @@ -111167,11 +129459,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of T3 in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - total venous blood T3 assay + total venous blood T3 assay + + An analyte assay that measures the abundance of T3 in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total venous blood T3 assay @@ -111238,11 +129532,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in urine as part of a 24 hour order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - 24 hour urine protein assay + 24 hour urine protein assay + + An analyte assay that measures the abundance of protein in urine as part of a 24 hour order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + 24 hour urine protein assay @@ -111309,11 +129605,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - total venous blood cholesterol assay + total venous blood cholesterol assay + + An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total venous blood cholesterol assay @@ -111380,11 +129678,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of triglyceride in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood triglyceride assay + venous blood triglyceride assay + + An analyte assay that measures the abundance of triglyceride in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood triglyceride assay @@ -111438,11 +129738,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - tube 4 count cerebrospinal fluid cell count assay + tube 4 count cerebrospinal fluid cell count assay + + A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + tube 4 count cerebrospinal fluid cell count assay @@ -111509,11 +129811,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid protein assay + cerebrospinal fluid protein assay + + An analyte assay that measures the abundance of protein in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid protein assay @@ -111580,11 +129884,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid glucose assay + cerebrospinal fluid glucose assay + + An analyte assay that measures the abundance of glucose in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid glucose assay @@ -111638,11 +129944,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - tube 1 count cerebrospinal fluid cell count assay + tube 1 count cerebrospinal fluid cell count assay + + A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + tube 1 count cerebrospinal fluid cell count assay @@ -111709,11 +130017,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood dehydroepiandrosterone assay + venous blood dehydroepiandrosterone assay + + An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood dehydroepiandrosterone assay @@ -111780,11 +130090,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of cortisol in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood cortisol assay + venous blood cortisol assay + + An analyte assay that measures the abundance of cortisol in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood cortisol assay @@ -111851,11 +130163,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood sodium assay + ABL90 panel arterial blood sodium assay + + An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood sodium assay @@ -111922,11 +130236,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood oxygen assay + ABL90 panel arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood oxygen assay @@ -111993,11 +130309,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood glucose assay + ABL90 panel arterial blood glucose assay + + An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood glucose assay @@ -112051,11 +130369,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures lactic acid in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood lactic acid assay + ABL90 panel arterial blood lactic acid assay + + An assay that measures lactic acid in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood lactic acid assay @@ -112122,11 +130442,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood hemoglobin assay + ABL90 panel arterial blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood hemoglobin assay @@ -112193,11 +130515,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood chloride assay + ABL90 panel arterial blood chloride assay + + An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood chloride assay @@ -112264,11 +130588,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood carbon dioxide assay + ABL90 panel arterial blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood carbon dioxide assay @@ -112322,11 +130648,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood hematocrit assay + ABL90 panel arterial blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood hematocrit assay @@ -112393,11 +130721,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood calcium assay + ABL90 panel arterial blood calcium assay + + An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood calcium assay @@ -112451,11 +130781,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures temperature in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood temperature assay + ABL90 panel arterial blood temperature assay + + An assay that measures temperature in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood temperature assay @@ -112522,11 +130854,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood bicarbonate assay + ABL90 panel arterial blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood bicarbonate assay @@ -112593,11 +130927,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood potassium assay + ABL90 panel arterial blood potassium assay + + An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood potassium assay @@ -112651,11 +130987,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood promyelocyte count assay + CBC with manual differential venous blood promyelocyte count assay + + A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood promyelocyte count assay @@ -112722,11 +131060,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood glucose assay + ABL90 panel venous blood glucose assay + + An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood glucose assay @@ -112793,11 +131133,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood hemoglobin assay + ABL90 panel venous blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood hemoglobin assay @@ -112864,11 +131206,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood ionized calcium assay + ABL90 panel venous blood ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood ionized calcium assay @@ -112935,11 +131279,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood carbon dioxide assay + ABL90 panel venous blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood carbon dioxide assay @@ -112993,11 +131339,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood hematocrit assay + ABL90 panel venous blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood hematocrit assay @@ -113064,11 +131412,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood sodium assay + ABL90 panel venous blood sodium assay + + An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood sodium assay @@ -113135,11 +131485,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood oxygen assay + ABL90 panel venous blood oxygen assay + + An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood oxygen assay @@ -113206,11 +131558,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood bicarbonate assay + ABL90 panel venous blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood bicarbonate assay @@ -113264,11 +131618,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures lactic acid in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood lactic acid assay + ABL90 panel venous blood lactic acid assay + + An assay that measures lactic acid in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood lactic acid assay @@ -113335,11 +131691,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood chloride assay + ABL90 panel venous blood chloride assay + + An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood chloride assay @@ -113406,11 +131764,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of T4 in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood T4 assay + venous blood T4 assay + + An analyte assay that measures the abundance of T4 in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood T4 assay @@ -113477,11 +131837,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of T4 in venous blood as part of a free order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - free venous blood T4 assay + free venous blood T4 assay + + An analyte assay that measures the abundance of T4 in venous blood as part of a free order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + free venous blood T4 assay @@ -113548,11 +131910,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood potassium assay + ABL90 panel venous blood potassium assay + + An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood potassium assay @@ -113619,11 +131983,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in urine - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - urine sodium assay + urine sodium assay + + An analyte assay that measures the abundance of sodium in urine + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + urine sodium assay @@ -113690,11 +132056,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bone profile venous blood albumin assay + bone profile venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bone profile venous blood albumin assay @@ -113761,11 +132129,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bone profile venous blood calcium assay + bone profile venous blood calcium assay + + An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bone profile venous blood calcium assay @@ -113832,11 +132202,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bone profile venous blood human alkaline phosphatase assay + bone profile venous blood human alkaline phosphatase assay + + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bone profile venous blood human alkaline phosphatase assay @@ -113903,11 +132275,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bone profile venous blood protein assay + bone profile venous blood protein assay + + An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bone profile venous blood protein assay @@ -113974,11 +132348,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bone profile venous blood phosphate assay + bone profile venous blood phosphate assay + + An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bone profile venous blood phosphate assay @@ -114045,11 +132421,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABG/electrolytes arterial blood carbon dioxide assay + ABG/electrolytes arterial blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABG/electrolytes arterial blood carbon dioxide assay @@ -114116,11 +132494,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABG/electrolytes arterial blood oxygen assay + ABG/electrolytes arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABG/electrolytes arterial blood oxygen assay @@ -114187,11 +132567,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABG/electrolytes arterial blood ionized calcium assay + ABG/electrolytes arterial blood ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABG/electrolytes arterial blood ionized calcium assay @@ -114245,11 +132627,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with automated differential venous blood nucleated RBC count assay + CBC with automated differential venous blood nucleated RBC count assay + + A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with automated differential venous blood nucleated RBC count assay @@ -114316,11 +132700,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel venous blood methemoglobin assay + ABL90 panel venous blood methemoglobin assay + + An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel venous blood methemoglobin assay @@ -114387,11 +132773,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ABL90 panel arterial blood methemoglobin assay + ABL90 panel arterial blood methemoglobin assay + + An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ABL90 panel arterial blood methemoglobin assay @@ -114458,11 +132846,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of valproic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood valproic acid assay + venous blood valproic acid assay + + An analyte assay that measures the abundance of valproic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood valproic acid assay @@ -114529,11 +132919,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - high sensitivity cardiac/neonatal venous blood c-reactive protein assay + high sensitivity cardiac/neonatal venous blood c-reactive protein assay + + An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + high sensitivity cardiac/neonatal venous blood c-reactive protein assay @@ -114600,11 +132992,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - POC arterial blood creatinine assay + POC arterial blood creatinine assay + + An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + POC arterial blood creatinine assay @@ -114671,11 +133065,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood bicarbonate assay + GEM4000 ANLCOOX arterial blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood bicarbonate assay @@ -114742,11 +133138,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood oxygen assay + GEM4000 ANLCOOX arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood oxygen assay @@ -114800,11 +133198,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood hematocrit assay + GEM4000 ANLCOOX arterial blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood hematocrit assay @@ -114858,11 +133258,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood temperature assay + GEM4000 ANLCOOX arterial blood temperature assay + + An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood temperature assay @@ -114929,11 +133331,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood hemoglobin assay + GEM4000 ANLCOOX arterial blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood hemoglobin assay @@ -115000,11 +133404,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood potassium assay + GEM4000 ANLCOOX arterial blood potassium assay + + An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood potassium assay @@ -115071,11 +133477,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood glucose assay + GEM4000 ANLCOOX arterial blood glucose assay + + An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood glucose assay @@ -115142,11 +133550,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood ionized calcium assay + GEM4000 ANLCOOX arterial blood ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood ionized calcium assay @@ -115213,11 +133623,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood carbon dioxide assay + GEM4000 ANLCOOX arterial blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood carbon dioxide assay @@ -115284,11 +133696,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4000 ANLCOOX arterial blood sodium assay + GEM4000 ANLCOOX arterial blood sodium assay + + An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4000 ANLCOOX arterial blood sodium assay @@ -115355,11 +133769,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - ionized venous blood calcium assay + ionized venous blood calcium assay + + An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + ionized venous blood calcium assay @@ -115426,11 +133842,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood hemoglobin assay + venous blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood hemoglobin assay @@ -115484,11 +133902,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood megakaryocyte count assay + CBC with manual differential venous blood megakaryocyte count assay + + A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood megakaryocyte count assay @@ -115555,11 +133975,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - non-cardiac venous blood c-reactive protein assay + non-cardiac venous blood c-reactive protein assay + + An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + non-cardiac venous blood c-reactive protein assay @@ -115626,11 +134048,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - intraoperative venous blood PTH assay + intraoperative venous blood PTH assay + + An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + intraoperative venous blood PTH assay @@ -115697,11 +134121,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of parathyroid hormone in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood parathyroid hormone assay + venous blood parathyroid hormone assay + + An analyte assay that measures the abundance of parathyroid hormone in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood parathyroid hormone assay @@ -115768,11 +134194,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in bodily fluid as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - total bodily fluid protein assay + total bodily fluid protein assay + + An analyte assay that measures the abundance of protein in bodily fluid as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total bodily fluid protein assay @@ -115839,11 +134267,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bodily fluid glucose assay + bodily fluid glucose assay + + An analyte assay that measures the abundance of glucose in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bodily fluid glucose assay @@ -115897,11 +134327,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of cells in bodily fluid as part of a count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - count bodily fluid cell count assay + count bodily fluid cell count assay + + A cytometry assay that measures the count of cells in bodily fluid as part of a count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + count bodily fluid cell count assay @@ -115955,11 +134387,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - manual differential bodily fluid segmented neutrophil count assay + manual differential bodily fluid segmented neutrophil count assay + + A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + manual differential bodily fluid segmented neutrophil count assay @@ -116013,11 +134447,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - manual differential bodily fluid mesothelial cell count assay + manual differential bodily fluid mesothelial cell count assay + + A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + manual differential bodily fluid mesothelial cell count assay @@ -116071,11 +134507,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - manual differential bodily fluid monocyte count assay + manual differential bodily fluid monocyte count assay + + A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + manual differential bodily fluid monocyte count assay @@ -116129,11 +134567,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - manual differential bodily fluid lymphocyte count assay + manual differential bodily fluid lymphocyte count assay + + A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + manual differential bodily fluid lymphocyte count assay @@ -116187,11 +134627,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - manual differential bodily fluid macrophage count assay + manual differential bodily fluid macrophage count assay + + A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + manual differential bodily fluid macrophage count assay @@ -116245,11 +134687,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - manual differential bodily fluid basophil count assay + manual differential bodily fluid basophil count assay + + A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + manual differential bodily fluid basophil count assay @@ -116303,11 +134747,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - manual differential bodily fluid eosinophil count assay + manual differential bodily fluid eosinophil count assay + + A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + manual differential bodily fluid eosinophil count assay @@ -116374,11 +134820,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver function venous blood bilirubin assay + liver function venous blood bilirubin assay + + An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver function venous blood bilirubin assay @@ -116445,11 +134893,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver function venous blood alanine aminotransferase assay + liver function venous blood alanine aminotransferase assay + + An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver function venous blood alanine aminotransferase assay @@ -116516,11 +134966,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver function venous blood human aspartate aminotransferase assay + liver function venous blood human aspartate aminotransferase assay + + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver function venous blood human aspartate aminotransferase assay @@ -116587,11 +135039,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver function venous blood albumin assay + liver function venous blood albumin assay + + An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver function venous blood albumin assay @@ -116658,11 +135112,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of protein in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver function venous blood protein assay + liver function venous blood protein assay + + An analyte assay that measures the abundance of protein in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver function venous blood protein assay @@ -116729,11 +135185,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver function venous blood human alkaline phosphatase assay + liver function venous blood human alkaline phosphatase assay + + An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver function venous blood human alkaline phosphatase assay @@ -116800,11 +135258,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - vitamin B12 and Folate venous blood folic acid assay + vitamin B12 and Folate venous blood folic acid assay + + An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + vitamin B12 and Folate venous blood folic acid assay @@ -116858,11 +135318,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of cells in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bodily fluid cell count assay + bodily fluid cell count assay + + A cytometry assay that measures the count of cells in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bodily fluid cell count assay @@ -116916,11 +135378,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of reticulocytes in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood reticulocyte count assay + venous blood reticulocyte count assay + + A cytometry assay that measures the count of reticulocytes in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood reticulocyte count assay @@ -116987,11 +135451,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of cholesterol in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bodily fluid cholesterol assay + bodily fluid cholesterol assay + + An analyte assay that measures the abundance of cholesterol in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bodily fluid cholesterol assay @@ -117058,11 +135524,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - TSH reflex Free T4 venous blood thyroid stimulating hormone assay + TSH reflex Free T4 venous blood thyroid stimulating hormone assay + + An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + TSH reflex Free T4 venous blood thyroid stimulating hormone assay @@ -117129,11 +135597,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - direct venous blood bilirubin assay + direct venous blood bilirubin assay + + An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + direct venous blood bilirubin assay @@ -117200,11 +135670,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of T3 in venous blood as part of a free order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - free venous blood T3 assay + free venous blood T3 assay + + An analyte assay that measures the abundance of T3 in venous blood as part of a free order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + free venous blood T3 assay @@ -117271,11 +135743,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of albumin in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bodily fluid albumin assay + bodily fluid albumin assay + + An analyte assay that measures the abundance of albumin in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bodily fluid albumin assay @@ -117342,11 +135816,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of triglyceride in bodily fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - bodily fluid triglyceride assay + bodily fluid triglyceride assay + + An analyte assay that measures the abundance of triglyceride in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bodily fluid triglyceride assay @@ -117400,11 +135876,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hemoglobin and hematocrit venous blood hematocrit assay + hemoglobin and hematocrit venous blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hemoglobin and hematocrit venous blood hematocrit assay @@ -117471,11 +135949,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - hemoglobin and hematocrit venous blood hemoglobin assay + hemoglobin and hematocrit venous blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + hemoglobin and hematocrit venous blood hemoglobin assay @@ -117542,11 +136022,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ionized calcium in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood ionized calcium assay + venous blood ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood ionized calcium assay @@ -117600,11 +136082,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures temperature in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood temperature assay + venous blood temperature assay + + An assay that measures temperature in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood temperature assay @@ -117671,11 +136155,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood bicarbonate assay + venous blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood bicarbonate assay @@ -117742,11 +136228,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood oxygen assay + venous blood oxygen assay + + An analyte assay that measures the abundance of oxygen in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood oxygen assay @@ -117800,11 +136288,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures osmolality in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood osmolality assay + venous blood osmolality assay + + An assay that measures osmolality in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood osmolality assay @@ -117858,11 +136348,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver fibrosis (chronic viral hepatitis) venous blood platelet count assay + liver fibrosis (chronic viral hepatitis) venous blood platelet count assay + + A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver fibrosis (chronic viral hepatitis) venous blood platelet count assay @@ -117929,11 +136421,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of T3 in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood T3 assay + venous blood T3 assay + + An analyte assay that measures the abundance of T3 in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood T3 assay @@ -117987,11 +136481,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood neutrophil count assay + CBC with manual differential venous blood neutrophil count assay + + A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood neutrophil count assay @@ -118058,11 +136554,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - creatinine clearance urine creatinine assay + creatinine clearance urine creatinine assay + + An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + creatinine clearance urine creatinine assay @@ -118129,11 +136627,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood beta hydroxybutryic acid assay + venous blood beta hydroxybutryic acid assay + + An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood beta hydroxybutryic acid assay @@ -118187,11 +136687,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of megakaryocytes in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood megakaryocyte count assay + venous blood megakaryocyte count assay + + A cytometry assay that measures the count of megakaryocytes in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood megakaryocyte count assay @@ -118245,11 +136747,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of nucleated RBCs in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood nucleated RBC count assay + venous blood nucleated RBC count assay + + A cytometry assay that measures the count of nucleated RBCs in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood nucleated RBC count assay @@ -118303,11 +136807,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of WBCs in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood WBC count assay + venous blood WBC count assay + + A cytometry assay that measures the count of WBCs in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood WBC count assay @@ -118361,11 +136867,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - automated count venous blood reticulocyte count assay + automated count venous blood reticulocyte count assay + + A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + automated count venous blood reticulocyte count assay @@ -118432,11 +136940,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - total venous blood homocysteine assay + total venous blood homocysteine assay + + An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total venous blood homocysteine assay @@ -118503,11 +137013,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of Ceruloplasmin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood Ceruloplasmin assay + venous blood Ceruloplasmin assay + + An analyte assay that measures the abundance of Ceruloplasmin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood Ceruloplasmin assay @@ -118574,11 +137086,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood bicarbonate assay + GEM4 arterial blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood bicarbonate assay @@ -118632,11 +137146,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures lactic acid in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood lactic acid assay + GEM4 arterial blood lactic acid assay + + An assay that measures lactic acid in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood lactic acid assay @@ -118703,11 +137219,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood hemoglobin assay + GEM4 arterial blood hemoglobin assay + + An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood hemoglobin assay @@ -118774,11 +137292,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood sodium assay + GEM4 arterial blood sodium assay + + An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood sodium assay @@ -118845,11 +137365,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood potassium assay + GEM4 arterial blood potassium assay + + An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood potassium assay @@ -118903,11 +137425,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An assay that measures temperature in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood temperature assay + GEM4 arterial blood temperature assay + + An assay that measures temperature in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood temperature assay @@ -118974,11 +137498,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood glucose assay + GEM4 arterial blood glucose assay + + An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood glucose assay @@ -119045,11 +137571,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood oxygen assay + GEM4 arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood oxygen assay @@ -119103,11 +137631,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood hematocrit assay + GEM4 arterial blood hematocrit assay + + A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood hematocrit assay @@ -119174,11 +137704,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood ionized calcium assay + GEM4 arterial blood ionized calcium assay + + An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood ionized calcium assay @@ -119245,11 +137777,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood carbon dioxide assay + GEM4 arterial blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood carbon dioxide assay @@ -119303,11 +137837,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - liver fibrosis (NAFLD) venous blood platelet count assay + liver fibrosis (NAFLD) venous blood platelet count assay + + A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver fibrosis (NAFLD) venous blood platelet count assay @@ -119374,11 +137910,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood beta hydroxybutric acid assay + venous blood beta hydroxybutric acid assay + + An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood beta hydroxybutric acid assay @@ -119432,11 +137970,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - CBC with manual differential venous blood plasma cell count assay + CBC with manual differential venous blood plasma cell count assay + + A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + CBC with manual differential venous blood plasma cell count assay @@ -119503,11 +138043,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of erythropoietin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood erythropoietin assay + venous blood erythropoietin assay + + An analyte assay that measures the abundance of erythropoietin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood erythropoietin assay @@ -119574,11 +138116,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - blood gas arterial blood oxygen assay + blood gas arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + blood gas arterial blood oxygen assay @@ -119645,11 +138189,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - blood gas arterial blood bicarbonate assay + blood gas arterial blood bicarbonate assay + + An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + blood gas arterial blood bicarbonate assay @@ -119716,11 +138262,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - blood gas arterial blood carbon dioxide assay + blood gas arterial blood carbon dioxide assay + + An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + blood gas arterial blood carbon dioxide assay @@ -119787,11 +138335,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - free/total venous blood PSA assay + free/total venous blood PSA assay + + An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + free/total venous blood PSA assay @@ -119845,11 +138395,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid lymphocyte count assay + cerebrospinal fluid lymphocyte count assay + + A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid lymphocyte count assay @@ -119903,11 +138455,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid segmented neutrophil count assay + cerebrospinal fluid segmented neutrophil count assay + + A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid segmented neutrophil count assay @@ -119961,11 +138515,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid mesothelial cell count assay + cerebrospinal fluid mesothelial cell count assay + + A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid mesothelial cell count assay @@ -120019,11 +138575,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of macrophages in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid macrophage count assay + cerebrospinal fluid macrophage count assay + + A cytometry assay that measures the count of macrophages in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid macrophage count assay @@ -120077,11 +138635,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of basophils in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid basophil count assay + cerebrospinal fluid basophil count assay + + A cytometry assay that measures the count of basophils in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid basophil count assay @@ -120135,11 +138695,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of monocytes in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid monocyte count assay + cerebrospinal fluid monocyte count assay + + A cytometry assay that measures the count of monocytes in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid monocyte count assay @@ -120193,11 +138755,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A cytometry assay that measures the count of eosinophils in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid eosinophil count assay + cerebrospinal fluid eosinophil count assay + + A cytometry assay that measures the count of eosinophils in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid eosinophil count assay @@ -120264,11 +138828,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of beta-2-microglobulin in venous blood - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - venous blood beta-2-microglobulin assay + venous blood beta-2-microglobulin assay + + An analyte assay that measures the abundance of beta-2-microglobulin in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood beta-2-microglobulin assay @@ -120335,11 +138901,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel reflex direct venous blood low density lipoprotein assay + lipid panel reflex direct venous blood low density lipoprotein assay + + An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lipid panel reflex direct venous blood low density lipoprotein assay @@ -120406,11 +138974,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel reflex direct venous blood triglyceride assay + lipid panel reflex direct venous blood triglyceride assay + + An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lipid panel reflex direct venous blood triglyceride assay @@ -120477,11 +139047,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel reflex direct venous blood cholesterol assay + lipid panel reflex direct venous blood cholesterol assay + + An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lipid panel reflex direct venous blood cholesterol assay @@ -120548,11 +139120,13 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel reflex direct venous blood high density lipoprotein assay + lipid panel reflex direct venous blood high density lipoprotein assay + + An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + lipid panel reflex direct venous blood high density lipoprotein assay @@ -120625,356 +139199,1403 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - Although a similar pooled clone sequencing method has recently been described by others for metagenome-derived medium-insert plasmids and large-insert fosmids, to our knowledge, we are the first to report the pooled strategy for sequencing of large-insert metagenomic clones while also critically evaluating the performance of this pooled strategy by comparing the results to barcoded reference sequences of the same clones. - A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. - Dan Berrios, ORCID: 0000-0003-4312-9552 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049660/ - https://github.com/obi-ontology/obi/issues/1106 - Bonita Lam - pooled clone sequencing assay + pooled clone sequencing assay + Although a similar pooled clone sequencing method has recently been described by others for metagenome-derived medium-insert plasmids and large-insert fosmids, to our knowledge, we are the first to report the pooled strategy for sequencing of large-insert metagenomic clones while also critically evaluating the performance of this pooled strategy by comparing the results to barcoded reference sequences of the same clones. + + A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. + Dan Berrios, ORCID: 0000-0003-4312-9552 + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049660/ + https://github.com/obi-ontology/obi/issues/1106 + Bonita Lam + pooled clone sequencing assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + chromium release assay + Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. + + An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. + IEDB + PlanAndPlannedProcess Branch + chromium release assay + + + + + + + + + clinical history + A series of statements representing health-relevant qualities of a patient and of a patient's family. + + clinical history + + + + + + + + + phenotype + A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. + + phenotype + + + + + + + + + disease + A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. + + disease + + + + + + + + + + + + + + + disease course + The totality of all processes through which a given disease instance is realized. + replace 'OBI:occurrence of disease', need to add logical definition +The axioms of OBI occurence of disease: +Equivalent classes: +realizes some disease +Superclasses: +'has part' some 'pathologic process' +'has participant' some + (organism + and ('has role' some 'host of immune response role')) +biological_process +realizes some 'host of immune response role' + + disease course + + + + + + + + + diagnosis + The representation of a conclusion of a diagnostic process. + + diagnosis + + + + + + + + + treatment + A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process + + treatment + + + + + + + + + fixed tissue specimen + A processed specimen that is the output of a fixation process. + + fixed tissue specimen + + + + + + + + + fixed tissue slide specimen + A fixed tissue specimen that is placed in a slide. + + fixed tissue slide specimen + + + + + + + + + health care provider role + A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. + + health care provider role + + + + + + + + + parasite organism + An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. + + parasite organism + + + + + + + + + Plasmodium gametocyte + A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes + + Plasmodium gametocyte + + + + + + + + + age + A time quality inhering in a bearer by virtue of how long the bearer has existed. + + age + + + + + + + + + fluorescence + A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together. + + fluorescence + + + + + + + + + composition + A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. + + composition + + + + + + + + + concentration of + A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. + + concentration of + + + + + + + + + biological sex + An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. + + biological sex + + + + + + + + + + morphology + A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. + + morphology + + + + + + + + + size + A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. + + size + + + + + + + + + length + A 1-D extent quality which is equal to the distance between two points. + + length + + + + + + + + + mass + A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. + + mass + + + + + + + + + position + A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. + + position + + + + + + + + + structure + A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. + + structure + + + + + + + + + temperature + A physical quality of the thermal energy of a system. + + temperature + + + + + + + + + time + A quality in which events occur in sequence. + + time + + + + + + + + + viability + An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. + + viability + + + + + + + + + behavioral quality + An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. + + behavioral quality + + + + + + + + + female + A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. + + female + + + + + + + + + male + A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. + + male + + + + + + + + + volume + A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. + + volume + + + + + + + + + physical quality + A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. + + physical quality + + + + + + + + + damage + A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled. + + damage + + + + + + + + + pressure + A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. + + pressure + + + + + + + + + diluted + A concentration which relatively low. + + diluted + + + + + + + + + damaged + A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. + + damaged + + + + + + + + + lateral to + A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. + + lateral to + + + + + + + + + ventral to + A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity. + + ventral to + + + + + + + + + dorsal to + A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. + + dorsal to + + + + + + + + + physical object quality + A quality which inheres in a continuant. + + physical object quality + + + + + + + + + electromagnetic (EM) radiation quality + A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. + + electromagnetic (EM) radiation quality + + + + + + + + + luminous flux + A scalar optical quality which obtains by the magnitude of the light emitted by the bearer. + + luminous flux + + + + + + + + + optical quality + An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. + + optical quality + + + + + + + + + bacterial mating type + A mating type that indicates whether the F plasmid has integrated into the chromosome. + + bacterial mating type + + + + + + + + + yeast mating type + A yeast mating type. + + yeast mating type + + + + + + + + + mixed sex + A biological sex quality inhering in a population of multiple sexes. + + mixed sex + + + + + + + + + biomaterial purity + A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. + + biomaterial purity + + + + + + + + + hermaphrodite + A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. + + hermaphrodite + + + + + + + + + a mating type (yeast) + A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. + + a mating type (yeast) + + + + + + + + + Saccharomyces cerevisiae mating type + A S. cerevisiae mating type. + + Saccharomyces cerevisiae mating type + + + + + + + + + Schizosaccharomyces pombe mating type + A S. pombe mating type determined by the gene configuration on the mat1 locus. + + Schizosaccharomyces pombe mating type + + + + + + + + + alpha mating type (yeast) + A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. + + alpha mating type (yeast) + + + + + + + + + h minus + A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. + + h minus + + + + + + + + + h plus + A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. + + h plus + + + + + + + + + F mating type + A bacterial mating type indicating the presence of F plasmid in a bacterial cell. + + F mating type + + + + + + + + + F minus mating type + A bacterial mating type indicating the absence of F plasmid in a bacterial cell. + + F minus mating type + + + + + + + + + ploidy + A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. + + ploidy + + + + + + + + + haploid + A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. + + haploid + + + + + + + + + polyploid + A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. + + polyploid + + + + + + + + + aneuploid + A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. + + aneuploid + + + + + + + + + euploid + A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. + + euploid + + + + + + + + + diploid + A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. + + diploid + + + + + + + + + cellular quality + A monadic quality of continuant that exists at the cellular level of organisation. + + cellular quality - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. - An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died. - IEDB - PlanAndPlannedProcess Branch - chromium release assay + + + alive + A viability quality inhering in a bearer by virtue of the bearer's condition before death. + + alive - + - + + + dead + A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. + + dead + - + - + + + quality of a solid + A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. + + quality of a solid + - + - - - - - - - - replace 'OBI:occurrence of disease', need to add logical definition -The axioms of OBI occurence of disease: -Equivalent classes: -realizes some disease -Superclasses: -'has part' some 'pathologic process' -'has participant' some - (organism - and ('has role' some 'host of immune response role')) -biological_process -realizes some 'host of immune response role' + + + quality of a gas + A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. + + quality of a gas - + - + + + quality of a liquid + A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. + + quality of a liquid + - + - + + + flow rate + A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. + + flow rate + - + - + + + anterior to + A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. + frontal + + anterior to + - + - + + + 3-D extent + A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. + + 3-D extent + - + - + + + radiation quality + A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. + + radiation quality + - + - + + + activity (of a radionuclide) + A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. + + activity (of a radionuclide) + - + - + + + radioactive + A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. + + radioactive + - + - + + + left side of + A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. + + left side of + - + - + + + right side of + A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. + + right side of + - + - + + + phenotypic sex + An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. + + phenotypic sex + - + - + + + mating type + A biological sex quality inhering in an individual or a population that undergo sexual reproduction. + + mating type + - + - + + + movement quality + A physical quality inhering in a bearer by virtue of the bearer's participation in movement. + + movement quality + - + + + + + frozen + A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. + + frozen + + + + + - + + + organismal quality + A quality that inheres in an entire organism or part of an organism. + + organismal quality + - + - - frontal + + + population quality + A quality that inheres in an entire population or part of a population. + + population quality - + - + + + osmolality + A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent. + + osmolality + - + - + + + molecular quality + A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. + + molecular quality + - + - + + + quality of a substance + A quality inhering in a bearer by virtue of its constitution. + + quality of a substance + - + + + handedness + A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. + + handedness + - + + + left handedness + Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. + + left handedness + - + + + right handedness + Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. + + right handedness + - + + + ambidextrous handedness + Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. + + ambidextrous handedness + + + + + + + + + fluid flow rate + A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. + + fluid flow rate + - antithrombin III is a protein + + protein + antithrombin III is a protein + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. + + protein - + + + CD4 molecule + A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. + + CD4 molecule + - + + + CD3 subunit with immunoglobulin domain + A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response. + + CD3 subunit with immunoglobulin domain + - + + + prostate-specific antigen + A protein that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof. + + prostate-specific antigen + - + + + antithrombin-III + A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof. + + antithrombin-III + - + + + double-stranded RNA-specific adenosine deaminase + A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof. + + double-stranded RNA-specific adenosine deaminase + - + + + adiponectin + A protein that is a translation product of the human ADIPOQ gene or a 1:1 ortholog thereof. + + adiponectin + - + + + albumin + A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof. + + albumin + - + + + beta-2-microglobulin + A protein that is a translation product of the human B2M gene or a 1:1 ortholog thereof. + + beta-2-microglobulin + - + + + ceruloplasmin + A protein that is a translation product of the human CP gene or a 1:1 ortholog thereof. + + ceruloplasmin + - + + + C-reactive protein + A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof. + + C-reactive protein + - + + + deoxyribonuclease-1 + A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof. + + deoxyribonuclease-1 + - + + + erythropoietin + A protein that is a translation product of the human EPO gene or a 1:1 ortholog thereof. + + erythropoietin + + + + + + + + + glial cell line-derived neurotrophic factor + A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof. + + glial cell line-derived neurotrophic factor + - + + + beta-globin + A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof. + + beta-globin + - + + + haptoglobin + A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof. + + haptoglobin + - + + + leptin + A protein that is a translation product of the human LEP gene or a 1:1 ortholog thereof. + + leptin + - + + + parathyroid hormone + A protein that is a translation product of the human PTH gene or a 1:1 ortholog thereof. + + parathyroid hormone + - + + + ribonuclease T2 + A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof. + + ribonuclease T2 + - + + + serotransferrin + A protein that is a translation product of the human TF gene or a 1:1 ortholog thereof. + + serotransferrin + - + + + transthyretin + A protein that is a translation product of the human TTR gene or a 1:1 ortholog thereof. + + transthyretin + + @@ -120986,87 +140607,180 @@ realizes some 'host of immune response role' - Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule - ligase + DNA ligase + A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof. + Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule + ligase + + DNA ligase + + + + + + + + + T cell receptor co-receptor CD8 + A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. + + T cell receptor co-receptor CD8 - + + + guanyl-specific ribonuclease T1 + A protein that is a translation product of the Aspergillus oryzae RIB40 rntA gene or a 1:1 ortholog thereof. + + guanyl-specific ribonuclease T1 + - + + + nuclease S1 + A protein that is a translation product of the Aspergillus oryzae RIB40 nucS gene or a 1:1 ortholog thereof. + + nuclease S1 + - + + + ribonuclease U2 + A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof. + + ribonuclease U2 + - + + + ribonuclease V1 (cobra) + A protein with ribonuclease activity that is a constituent of cobra venom. + + ribonuclease V1 (cobra) + - + + + ribonuclease CL3 (chicken) + A protein with ribonuclease activity that is purified from chicken liver. + + ribonuclease CL3 (chicken) + - + + + cytosolic creatine kinase complex, MB-type + A cytosolic creatine kinase complex that is a heterodimer of a B-type subunit and an M-type subunit. + + cytosolic creatine kinase complex, MB-type + - + + + creatine kinase + A protein that contains a single ATP:guanido phosphotransferase N-terminal domain (Pfam:PF02807) followed by a single ATP:guanido phosphotransferase C-terminal catalytic domain (Pfam:PF00217). + + creatine kinase + - + + + protein-glutamine gamma-glutamyltransferase + + protein-glutamine gamma-glutamyltransferase + - + + + alanine aminotransferase + A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. + + alanine aminotransferase + - + + + lactate dehydrogenase complex + A protein-containing complex that is composed of four subunits of L-lactate dehydrogenase, cytoplasmic. + + lactate dehydrogenase complex + - + + + alkaline phosphatase (human) + A protein that is a translation product of any of the following alkaline phosphatase genes in human: ALPG (encoding the germinal form; GCAP), ALPP (encoding the placental form; PLAP), ALPI (encoding the intestinal form; IAP), and ALPL (encoding the tissue non-specific form; TNAP). + + alkaline phosphatase (human) + - + + + aspartate aminotransferase (human) + A protein that is a translation product of any of the following genes in human: GOT1/GOT2. + + aspartate aminotransferase (human) + - + + + hemoglobin A1c + A hemoglobin complex that is composed of at least one beta-N-1-deoxy fructosyl hemoglobin subunit, in which the glycan is attached to the N-terminal valine (after initiator methionine removal) of one or both beta subunits. + + hemoglobin A1c + @@ -121075,12 +140789,12 @@ realizes some 'host of immune response role' - A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. - Group: OBI - molecular tracer role - OBI developer call, 3-12-12 + A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. + Group: OBI + molecular tracer role + OBI developer call, 3-12-12 - obsolete molecular label role + obsolete molecular label role true @@ -121091,12 +140805,12 @@ realizes some 'host of immune response role' - A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay - Group: OBI - molecular tracer - OBI developer call, 3-12-12 + A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay + Group: OBI + molecular tracer + OBI developer call, 3-12-12 - obsolete molecular label + obsolete molecular label true @@ -121105,8 +140819,13 @@ realizes some 'host of immune response role' - primary structure of sequence macromolecule - sequence + + region + A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. + primary structure of sequence macromolecule + sequence + + region @@ -121114,675 +140833,1614 @@ realizes some 'host of immune response role' - polypeptide sequence + + polypeptide + A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. + polypeptide sequence + + polypeptide - + + + supercontig + One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. + + supercontig + - + + + contig + A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. + + contig + + + + + + + + + TF_binding_site + A DNA site where a transcription factor binds. + + TF_binding_site + - + + + miRNA + Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. + + miRNA + - + + + sequence_assembly + A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. + + sequence_assembly + - + + + circular + A quality of a nucleotide polymer that has no terminal nucleotide residues. + + circular + - + + + assembly + A region of the genome of known length that is composed by ordering and aligning two or more different regions. + + assembly + + + + + + + + + experimental_feature + A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. + + experimental_feature + + + + + + + + + regulatory_region + A region of sequence that is involved in the control of a biological process. + + regulatory_region + - + + + uterine cervix + Lower, narrow portion of the uterus where it joins with the top end of the vagina. + + uterine cervix + - + + + pituitary gland + The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. + + pituitary gland + - + + + lymph node + Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. + + lymph node + - + + + urethra + The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. + + urethra + - + + + life cycle stage + A spatiotemporal region encompassing some part of the life cycle of an organism. + + life cycle stage + - + + + mouth + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). + + mouth + - + + + amniotic fluid + Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. + + amniotic fluid + - + + + blood + A fluid that is composed of blood plasma and erythrocytes. + + blood + - + + + breast + The upper ventral region of the torso of an organism. + + breast + - + + + + cervical mucus + A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. + + cervical mucus + - + + + throat + In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. + + throat + - + + + renal medulla + The inner portion of the kidney consisting of the renal pyramids. + + renal medulla + + + + + + + + + organism substance + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. + + organism substance + - + + + material anatomical entity + Anatomical entity that has mass. + + material anatomical entity + - + + + testis + A gonad of a male animal. A gonad produces and releases sperm. + + testis + - + + + anatomical cluster + Anatomical group that has its parts adjacent to one another. + + anatomical cluster + - + + + tissue + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + + tissue + + + + + + + + + multi-tissue structure + Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. + + multi-tissue structure + + + + + + + + + epithelium + Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. + + epithelium + - + + + stomach + An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. + + stomach + - + + + aorta + The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. + + aorta + - + + + heart + A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. + + heart + - + + + brain + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. + + brain + - + + + + cerebral cortex + The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. + + cerebral cortex + - + + + eye + An organ that detects light. + + eye + - + + + ovary + The gonad of a female organism which contains germ cells. + + ovary + - + + + uterus + The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. + + uterus + - + + + vagina + A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. + + vagina + - + + + respiratory system + Functional system which consists of structures involved in respiration. + + respiratory system + - + + + adipose tissue + Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. + + adipose tissue + - + + + strand of hair + A filament, mostly protein, that grows from follicles found in the dermis[WP]. + + strand of hair + - + + + rectum + The terminal portion of the intestinal tube, terminating with the anus. + + rectum + - + + + pleural fluid + Transudate contained in the pleural cavity. + + pleural fluid + - + + + urine + Excretion that is the output of a kidney. + + urine + - + + + + sweat + Secretion produced by a sweat gland. + + sweat + - + + + + synovial fluid + Joint fluid is a transudate of plasma that is actively secreted by synovial cells. + + synovial fluid + - + + + + skeletal muscle tissue + Muscle tissue that consists primarily of skeletal muscle fibers. + + skeletal muscle tissue + - + + + colon + A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. + + colon + - + + + sigmoid colon + The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. + + sigmoid colon + - + + + cortex of kidney + Outer cortical portion of the kidney, between the renal capsule and the renal medulla. + + cortex of kidney + - + + + urinary bladder + Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. + + urinary bladder + - + + + pancreas + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. + + pancreas + - + + + + peritoneal fluid + Transudate contained in the peritoneal cavity. + + peritoneal fluid + - + + + + tibial nerve + The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. + + tibial nerve + - + + + cerebrospinal fluid + A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. + + cerebrospinal fluid + + + + + + + + + arm + The part of the forelimb extending from the shoulder to the autopod[cjm]. + + arm + + + + + + + + + digestive tract + A tube extending from the mouth to the anus. + + digestive tract + - + + + upper respiratory tract + The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. + + upper respiratory tract + - + + + lower respiratory tract + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. + + lower respiratory tract + - + + + cheek + A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. + + cheek + - + + + coronary artery + An artery that supplies the myocardium. + + coronary artery + - + + + vein + Any of the tubular branching vessels that carry blood from the capillaries toward the heart. + + vein + - + + + tongue + A muscular organ in the floor of the mouth. + + tongue + - + + + nasopharynx + The section of the pharynx that lies above the soft palate. + + nasopharynx + - + + + oropharynx + The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. + + oropharynx + - + + + vitreous humor + A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina. + + vitreous humor + - + + + nasal cavity mucosa + The mucous membrane that lines the nasal cavity[MP]. + + nasal cavity mucosa + - + + + minor salivary gland + One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. + + minor salivary gland + - + + + saliva + A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. + + saliva + - + + + + caudate nucleus + Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. + + caudate nucleus + + + + + + + + + + putamen + Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion. + + putamen + - + + + + milk + An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. + + milk + - + + + semen + Organism substance that is composed of sperm cells suspended in seminal fluid. + + semen + - + + + + bile + Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. + + bile + - + + + placenta + Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. + + placenta + - + + + feces + Portion of semisolid bodily waste discharged through the anus[MW,modified]. + + feces + - + + + areola + Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. + + areola + - + + + + cerebellum + Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. + + cerebellum + - + + + thyroid gland + A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. + + thyroid gland + - + + + lung + Respiration organ that develops as an outpocketing of the esophagus. + + lung + - + + + dermis + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. + + dermis + - + + + hypodermis + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. + + hypodermis + - + + + skin of body + The organ covering the body that consists of the dermis and epidermis. + + skin of body + - + + + spleen + The organ that functions to filter blood and to store red corpuscles and platelets. + + spleen + - + + + liver + An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. + + liver + - + + + ileum + The portion of the small intestine that extends from the jejunum to the colon. + + ileum + - + + + integument + The dermis, epidermis and hypodermis. + + integument + - + + + + peritoneum + A serous membrane that lines the peritoneal cavity[VHOG,modified]. + + peritoneum + - + + + prostate gland + The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. + + prostate gland + - + + + adrenal gland + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. + + adrenal gland + - + + + + bone marrow + The soft tissue that fills the cavities of bones. + + bone marrow + + + + + + + + + lymph + Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. + + lymph + - + + + + pericardial fluid + Transudate contained in the pericardial cavity.[FMA]. + + pericardial fluid + - + + + tail + An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. + + tail + - + + + esophagus mucosa + A mucosa that is part of a esophagus [Automatically generated definition]. + + esophagus mucosa + + + + + + + + + left cerebral hemisphere + A cerebral hemisphere that is in the left side of a brain. + + left cerebral hemisphere + + + + + + + + + right cerebral hemisphere + A cerebral hemisphere that is in the right side of a brain. + + right cerebral hemisphere + - + + + trachea + The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. + + trachea + - + + + omentum + A fold of peritoneum originating at the stomach and supporting the viscera. + + omentum + - + + + + esophagus muscularis mucosa + A muscularis mucosa that is part of a esophagus. + + esophagus muscularis mucosa + - + + + mucosa of nasopharynx + A mucosa that is part of a nasopharynx [Automatically generated definition]. + + mucosa of nasopharynx + + + + + + + + + mucosa of oropharynx + A mucosa that is part of a oropharynx [Automatically generated definition]. + + mucosa of oropharynx + - + + + middle nasal concha + The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. + + middle nasal concha + - + + + bodily fluid + Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + + bodily fluid + - + + + respiratory system fluid/secretion + A portion of organism substance that secreted_by a respiratory system. + + respiratory system fluid/secretion + - + + + + atrium auricular region + A small conical pouch projections located on the upper anterior portion of each atrium of the heart. + + atrium auricular region + - + + + digestive system secreted substance + + digestive system secreted substance + - + + + chorionic villus + One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. + + chorionic villus + - + + + meconium + A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. + + meconium + - + + + sputum + Matter ejected from the lungs, bronchi, and trachea, through the mouth. + + sputum + - + + + tibial artery + The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. + + tibial artery + - + + + esophagogastric junction + The junction between the esophagus and the stomach epithelium. + + esophagogastric junction + - + + + + + omental fat pad + Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon. + + omental fat pad + - + + + umbilical cord blood + Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. + + umbilical cord blood + - + + + arterial blood + A blood that is part of a artery. + + arterial blood + - + + + venous blood + A blood that is part of a vein. + + venous blood + - + + + capillary blood + A blood that is part of a capillary. + + capillary blood + - + + + suprapubic skin + Area of skin in the hypoastric region of the abdomen. + + suprapubic skin + - + + + anterior nasal wall + Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule. + + anterior nasal wall + + + + + + + + + placental blood + Blood located in the placenta. + + placental blood + + + + + + + + + length unit + A unit which is a standard measure of the distance between two points. + + length unit + - + + + mass unit + A unit which is a standard measure of the amount of matter/energy of a physical object. + + mass unit + - + + + time unit + A unit which is a standard measure of the dimension in which events occur in sequence. + + time unit + - + + + temperature unit + + temperature unit + + + + + + + + + substance unit + + substance unit + - + + + concentration unit + + concentration unit + - + + + volume unit + + volume unit + + + + + + + + + frequency unit + + frequency unit + + + + + + + + + pressure unit + + pressure unit + + + + + + + + + volumetric flow rate unit + + volumetric flow rate unit + + + + + + + + + rate unit + + rate unit + + + + + + + + + vaccine + A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. + + vaccine + + + + + + + + + vaccination + a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response. + + vaccination + - Obsolete Class + Obsolete Class @@ -121804,19 +142462,43 @@ realizes some 'host of immune response role' + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + failed exploratory term + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete @@ -121826,7 +142508,10 @@ realizes some 'host of immune response role' - PERSON:Alan Ruttenberg + organizational term + Term created to ease viewing/sort terms for development purpose, and will not be included in a release + PERSON:Alan Ruttenberg + organizational term @@ -121836,6 +142521,9 @@ realizes some 'host of immune response role' + ready for release + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release @@ -121845,6 +142533,9 @@ realizes some 'host of immune response role' + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete @@ -121854,6 +142545,9 @@ realizes some 'host of immune response role' + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated @@ -121863,10 +142557,146 @@ realizes some 'host of immune response role' + pending final vetting + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + + obsolete_core + true + + + + + + + + + + placeholder removed + placeholder removed + + + + + terms merged + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + term imported + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + term split + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. + We expect to be able to mine these new reasons and add instances as required. + obsolete_other + true + + + + + + + + + universal + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + defined class + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + named class expression + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + to be replaced with external ontology term + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + requires discussion + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + @@ -121876,7 +142706,7 @@ realizes some 'host of immune response role' Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) person:Jennifer Fostel - web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf + web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf Transformation-ML @@ -121891,7 +142721,7 @@ realizes some 'host of immune response role' ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) person:Jennifer Fostel - web-page:http://www.isac-net.org/content/view/607/150/ + web-page:http://www.isac-net.org/content/view/607/150/ ACS @@ -121906,7 +142736,7 @@ realizes some 'host of immune response role' XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel - web-page:http://www.w3.org/XML/ + web-page:http://www.w3.org/XML/ XML @@ -121921,7 +142751,7 @@ realizes some 'host of immune response role' RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) person:Jennifer Fostel - web-page:http://www.w3.org/RDF/ + web-page:http://www.w3.org/RDF/ RDF @@ -121936,7 +142766,7 @@ realizes some 'host of immune response role' zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) person:Jennifer Fostel - web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ + web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ zip @@ -121951,7 +142781,7 @@ realizes some 'host of immune response role' tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) person:Jennifer Fostel - web-page:http://www.gnu.org/software/tar/manual/ + web-page:http://www.gnu.org/software/tar/manual/ tar @@ -121966,7 +142796,7 @@ realizes some 'host of immune response role' FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) person:Jennifer Fostel - web-page:http://www.fcspress.com/ + web-page:http://www.fcspress.com/ FCS @@ -121981,7 +142811,7 @@ realizes some 'host of immune response role' Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) person:Jennifer Fostel - web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf + web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML @@ -121996,7 +142826,7 @@ realizes some 'host of immune response role' Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) person:Jennifer Fostel - web-page:http://www.flowcyt.org/gating/ + web-page:http://www.flowcyt.org/gating/ Gating-ML @@ -122011,7 +142841,7 @@ realizes some 'host of immune response role' OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) person:Jennifer Fostel - web-page:http://www.w3.org/2004/OWL/ + web-page:http://www.w3.org/2004/OWL/ OWL @@ -122021,9 +142851,10 @@ realizes some 'host of immune response role' - obsolete_the supplier role of Affymetrix + obsolete_the supplier role of Affymetrix + - obsolete_the supplier role of Affymetrix + obsolete_the supplier role of Affymetrix true @@ -122034,10 +142865,11 @@ realizes some 'host of immune response role' - Affymetrix - Affymetrix supplied microarray - An organization which supplies technology, tools and protocols for use in high throughput applications - Affymetrix + Affymetrix + Affymetrix supplied microarray + + An organization which supplies technology, tools and protocols for use in high throughput applications + Affymetrix @@ -122046,9 +142878,10 @@ realizes some 'host of immune response role' - Thermo - Philippe Rocca-Serra - Thermo + Thermo + + Philippe Rocca-Serra + Thermo @@ -122057,9 +142890,10 @@ realizes some 'host of immune response role' - Waters - Philippe Rocca-Serra - Waters + Waters + + Philippe Rocca-Serra + Waters @@ -122068,9 +142902,10 @@ realizes some 'host of immune response role' - BIO-RAD - Philippe Rocca-Serra - BIO-RAD + BIO-RAD + + Philippe Rocca-Serra + BIO-RAD @@ -122079,9 +142914,10 @@ realizes some 'host of immune response role' - GenePattern hierarchical clustering - James Malone - GenePattern hierarchical clustering + GenePattern hierarchical clustering + + James Malone + GenePattern hierarchical clustering @@ -122090,9 +142926,10 @@ realizes some 'host of immune response role' - Ambion - Philippe Rocca-Serra - Ambion + Ambion + + Philippe Rocca-Serra + Ambion @@ -122101,9 +142938,10 @@ realizes some 'host of immune response role' - Helicos - Philippe Rocca-Serra - Helicos + Helicos + + Philippe Rocca-Serra + Helicos @@ -122112,9 +142950,10 @@ realizes some 'host of immune response role' - Roche - Philippe Rocca-Serra - Roche + Roche + + Philippe Rocca-Serra + Roche @@ -122123,9 +142962,10 @@ realizes some 'host of immune response role' - Illumina - Philippe Rocca-Serra - Illumina + Illumina + + Philippe Rocca-Serra + Illumina @@ -122134,8 +142974,9 @@ realizes some 'host of immune response role' - GenePattern PCA - GenePattern PCA + GenePattern PCA + + GenePattern PCA @@ -122145,11 +142986,12 @@ realizes some 'host of immune response role' - GenePattern module SVM - GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. - James Malone - Ryan Brinkman - GenePattern module SVM + GenePattern module SVM + + GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. + James Malone + Ryan Brinkman + GenePattern module SVM @@ -122158,9 +143000,10 @@ realizes some 'host of immune response role' - GenePattern k-nearest neighbors - James Malone - GenePattern k-nearest neighbors + GenePattern k-nearest neighbors + + James Malone + GenePattern k-nearest neighbors @@ -122169,8 +143012,9 @@ realizes some 'host of immune response role' - GenePattern LOOCV - GenePattern LOOCV + GenePattern LOOCV + + GenePattern LOOCV @@ -122179,9 +143023,10 @@ realizes some 'host of immune response role' - GenePattern k-means clustering - James Malone - GenePattern k-means clustering + GenePattern k-means clustering + + James Malone + GenePattern k-means clustering @@ -122190,9 +143035,10 @@ realizes some 'host of immune response role' - Agilent - Philippe Rocca-Serra - Agilent + Agilent + + Philippe Rocca-Serra + Agilent @@ -122202,11 +143048,12 @@ realizes some 'host of immune response role' - GenePattern module KMeansClustering - GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. - James Malone - PERSON: James Malone - GenePattern module KMeansClustering + GenePattern module KMeansClustering + + GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. + James Malone + PERSON: James Malone + GenePattern module KMeansClustering @@ -122215,9 +143062,10 @@ realizes some 'host of immune response role' - GenePattern CART - James Malone - GenePattern CART + GenePattern CART + + James Malone + GenePattern CART @@ -122228,9 +143076,10 @@ realizes some 'host of immune response role' - GenePattern module CARTXValidation - GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. - GenePattern module CARTXValidation + GenePattern module CARTXValidation + + GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. + GenePattern module CARTXValidation @@ -122239,9 +143088,10 @@ realizes some 'host of immune response role' - Li-Cor - Philippe Rocca-Serra - Li-Cor + Li-Cor + + Philippe Rocca-Serra + Li-Cor @@ -122250,9 +143100,10 @@ realizes some 'host of immune response role' - Bruker Corporation - Philippe Rocca-Serra - Bruker Corporation + Bruker Corporation + + Philippe Rocca-Serra + Bruker Corporation @@ -122261,11 +143112,12 @@ realizes some 'host of immune response role' - GenePattern module KNNXValidation - GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. - James Malone - PERSON: James Malone - GenePattern module KNNXValidation + GenePattern module KNNXValidation + + GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. + James Malone + PERSON: James Malone + GenePattern module KNNXValidation @@ -122275,8 +143127,9 @@ realizes some 'host of immune response role' - GenePattern module PeakMatch - GenePattern module PeakMatch + GenePattern module PeakMatch + + GenePattern module PeakMatch @@ -122286,10 +143139,11 @@ realizes some 'host of immune response role' - GenePattern module KNN - GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. - James Malone - GenePattern module KNN + GenePattern module KNN + + GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. + James Malone + GenePattern module KNN @@ -122299,11 +143153,12 @@ realizes some 'host of immune response role' - GenePattern module HierarchicalClustering - GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. - James Malone - PERSON: James Malone - GenePattern module HierarchicalClustering + GenePattern module HierarchicalClustering + + GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. + James Malone + PERSON: James Malone + GenePattern module HierarchicalClustering @@ -122312,9 +143167,10 @@ realizes some 'host of immune response role' - GenePattern SVM - James Malone - GenePattern SVM + GenePattern SVM + + James Malone + GenePattern SVM @@ -122323,9 +143179,10 @@ realizes some 'host of immune response role' - Applied Biosystems - Philippe Rocca-Serra - Applied Biosystems + Applied Biosystems + + Philippe Rocca-Serra + Applied Biosystems @@ -122335,11 +143192,12 @@ realizes some 'host of immune response role' - GenePattern module PCA - GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. - James Malone - PERSON: James Malone - GenePattern module PCA + GenePattern module PCA + + GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. + James Malone + PERSON: James Malone + GenePattern module PCA @@ -122348,10 +143206,11 @@ realizes some 'host of immune response role' - GenePattern peak matching - James Malone - Ryan Brinkman - GenePattern peak matching + GenePattern peak matching + + James Malone + Ryan Brinkman + GenePattern peak matching @@ -122360,9 +143219,10 @@ realizes some 'host of immune response role' - Bruker Daltonics - Philippe Rocca-Serra - Bruker Daltonics + Bruker Daltonics + + Philippe Rocca-Serra + Bruker Daltonics @@ -122371,10 +143231,11 @@ realizes some 'host of immune response role' - GenePattern HeatMapViewer data visualization - The GenePattern process of generating Heat Maps from clustered data. - James Malone - GenePattern HeatMapViewer data visualization + GenePattern HeatMapViewer data visualization + + The GenePattern process of generating Heat Maps from clustered data. + James Malone + GenePattern HeatMapViewer data visualization @@ -122383,10 +143244,11 @@ realizes some 'host of immune response role' - GenePattern HierarchicalClusteringViewer data visualization - The GenePattern process of generating hierarchical clustering visualization from clustered data. - James Malone - GenePattern HierarchicalClusteringViewer data visualization + GenePattern HierarchicalClusteringViewer data visualization + + The GenePattern process of generating hierarchical clustering visualization from clustered data. + James Malone + GenePattern HierarchicalClusteringViewer data visualization @@ -122396,10 +143258,11 @@ realizes some 'host of immune response role' - GenePattern module HeatMapViewer - A GenePattern software module which is used to generate a heatmap view of data. - James Malone - GenePattern module HeatMapViewer + GenePattern module HeatMapViewer + + A GenePattern software module which is used to generate a heatmap view of data. + James Malone + GenePattern module HeatMapViewer @@ -122409,10 +143272,11 @@ realizes some 'host of immune response role' - GenePattern module HierarchicalClusteringViewer - A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. - James Malone - GenePattern module HierarchicalClusteringViewer + GenePattern module HierarchicalClusteringViewer + + A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. + James Malone + GenePattern module HierarchicalClusteringViewer @@ -122421,10 +143285,10 @@ realizes some 'host of immune response role' - Sysmex Corporation, Kobe, Japan + Sysmex Corporation, Kobe, Japan - WEB:http://www.sysmex.com/@2009/08/06 - Sysmex Corporation, Kobe, Japan + WEB:http://www.sysmex.com/@2009/08/06 + Sysmex Corporation, Kobe, Japan @@ -122433,9 +143297,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Agilent + obsolete_the manufacturer role of Agilent + - obsolete_the manufacturer role of Agilent + obsolete_the manufacturer role of Agilent true @@ -122445,9 +143310,10 @@ realizes some 'host of immune response role' - obsolete_manufacturer role of Bruker Daltonics + obsolete_manufacturer role of Bruker Daltonics + - obsolete_manufacturer role of Bruker Daltonics + obsolete_manufacturer role of Bruker Daltonics true @@ -122457,9 +143323,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Thermo + obsolete_the manufacturer role of Thermo + - obsolete_the manufacturer role of Thermo + obsolete_the manufacturer role of Thermo true @@ -122469,9 +143336,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Li-Cor + obsolete_the manufacturer role of Li-Cor + - obsolete_the manufacturer role of Li-Cor + obsolete_the manufacturer role of Li-Cor true @@ -122481,9 +143349,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Roche + obsolete_the manufacturer role of Roche + - obsolete_the manufacturer role of Roche + obsolete_the manufacturer role of Roche true @@ -122493,9 +143362,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Ambion + obsolete_the manufacturer role of Ambion + - obsolete_the manufacturer role of Ambion + obsolete_the manufacturer role of Ambion true @@ -122505,9 +143375,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of BIO-RAD + obsolete_the manufacturer role of BIO-RAD + - obsolete_the manufacturer role of BIO-RAD + obsolete_the manufacturer role of BIO-RAD true @@ -122517,9 +143388,10 @@ realizes some 'host of immune response role' - obsolete_the regulator role of the FDA + obsolete_the regulator role of the FDA + - obsolete_the regulator role of the FDA + obsolete_the regulator role of the FDA true @@ -122529,9 +143401,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Illumina + obsolete_the manufacturer role of Illumina + - obsolete_the manufacturer role of Illumina + obsolete_the manufacturer role of Illumina true @@ -122541,9 +143414,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Helicos + obsolete_the manufacturer role of Helicos + - obsolete_the manufacturer role of Helicos + obsolete_the manufacturer role of Helicos true @@ -122553,9 +143427,10 @@ realizes some 'host of immune response role' - obsolete_manufacturer role of Bruker Corporation + obsolete_manufacturer role of Bruker Corporation + - obsolete_manufacturer role of Bruker Corporation + obsolete_manufacturer role of Bruker Corporation true @@ -122565,9 +143440,10 @@ realizes some 'host of immune response role' - obsolete_the manufacturer role of Waters + obsolete_the manufacturer role of Waters + - obsolete_the manufacturer role of Waters + obsolete_the manufacturer role of Waters true @@ -122577,9 +143453,10 @@ realizes some 'host of immune response role' - obsolete_manufacturer role of applied biosystems + obsolete_manufacturer role of applied biosystems + - obsolete_manufacturer role of applied biosystems + obsolete_manufacturer role of applied biosystems true @@ -122589,9 +143466,10 @@ realizes some 'host of immune response role' - U.S. Food and Drug Administration - FDA - U.S. Food and Drug Administration + U.S. Food and Drug Administration + + FDA + U.S. Food and Drug Administration @@ -122600,8 +143478,9 @@ realizes some 'host of immune response role' - right handed - right handed + right handed + + right handed @@ -122610,8 +143489,9 @@ realizes some 'host of immune response role' - ambidexterous - ambidexterous + ambidexterous + + ambidexterous @@ -122620,8 +143500,9 @@ realizes some 'host of immune response role' - left handed - left handed + left handed + + left handed @@ -122630,13 +143511,14 @@ realizes some 'host of immune response role' - Edingburgh handedness inventory + Edingburgh handedness inventory + The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. - PERSON:Alan Ruttenberg - PERSON:Jessica Turner - PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 - WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html - Edingburgh handedness inventory + PERSON:Alan Ruttenberg + PERSON:Jessica Turner + PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 + WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html + Edingburgh handedness inventory @@ -122645,10 +143527,11 @@ realizes some 'host of immune response role' - eBioscience - Karin Breuer - WEB:http://www.ebioscience.com/@2011/04/11 - eBioscience + eBioscience + + Karin Breuer + WEB:http://www.ebioscience.com/@2011/04/11 + eBioscience @@ -122657,10 +143540,11 @@ realizes some 'host of immune response role' - Cytopeia - Karin Breuer - WEB:http://www.cytopeia.com/@2011/04/11 - Cytopeia + Cytopeia + + Karin Breuer + WEB:http://www.cytopeia.com/@2011/04/11 + Cytopeia @@ -122669,10 +143553,11 @@ realizes some 'host of immune response role' - Exalpha Biological - Karin Breuer - WEB:http://www.exalpha.com/@2011/04/11 - Exalpha Biological + Exalpha Biological + + Karin Breuer + WEB:http://www.exalpha.com/@2011/04/11 + Exalpha Biological @@ -122681,10 +143566,11 @@ realizes some 'host of immune response role' - Apogee Flow Systems - Karin Breuer - WEB:http://www.apogeeflow.com/@2011/04/11 - Apogee Flow Systems + Apogee Flow Systems + + Karin Breuer + WEB:http://www.apogeeflow.com/@2011/04/11 + Apogee Flow Systems @@ -122693,10 +143579,11 @@ realizes some 'host of immune response role' - Exbio Antibodies - Karin Breuer - WEB:http://www.exbio.cz/@2011/04/11 - Exbio Antibodies + Exbio Antibodies + + Karin Breuer + WEB:http://www.exbio.cz/@2011/04/11 + Exbio Antibodies @@ -122705,10 +143592,11 @@ realizes some 'host of immune response role' - Becton Dickinson (BD Biosciences) - Karin Breuer - WEB:http://www.bdbiosciences.com/@2011/04/11 - Becton Dickinson (BD Biosciences) + Becton Dickinson (BD Biosciences) + + Karin Breuer + WEB:http://www.bdbiosciences.com/@2011/04/11 + Becton Dickinson (BD Biosciences) @@ -122717,10 +143605,11 @@ realizes some 'host of immune response role' - Dako Cytomation - Karin Breuer - WEB:http://www.dakousa.com/@2011/04/11 - Dako Cytomation + Dako Cytomation + + Karin Breuer + WEB:http://www.dakousa.com/@2011/04/11 + Dako Cytomation @@ -122729,10 +143618,11 @@ realizes some 'host of immune response role' - Millipore - Karin Breuer - WEB:http://www.guavatechnologies.com/@2011/04/11 - Millipore + Millipore + + Karin Breuer + WEB:http://www.guavatechnologies.com/@2011/04/11 + Millipore @@ -122741,10 +143631,11 @@ realizes some 'host of immune response role' - Antigenix - Karin Breuer - WEB:http://www.antigenix.com/@2011/04/11 - Antigenix + Antigenix + + Karin Breuer + WEB:http://www.antigenix.com/@2011/04/11 + Antigenix @@ -122753,10 +143644,11 @@ realizes some 'host of immune response role' - Partec - Karin Breuer - WEB:http://www.partec.de/@2011/04/11 - Partec + Partec + + Karin Breuer + WEB:http://www.partec.de/@2011/04/11 + Partec @@ -122765,10 +143657,11 @@ realizes some 'host of immune response role' - Beckman Coulter - Karin Breuer - WEB:http://www.beckmancoulter.com/@2011/04/11 - Beckman Coulter + Beckman Coulter + + Karin Breuer + WEB:http://www.beckmancoulter.com/@2011/04/11 + Beckman Coulter @@ -122777,10 +143670,11 @@ realizes some 'host of immune response role' - Advanced Instruments Inc. (AI Companies) - Karin Breuer - WEB:http://www.aicompanies.com/@2011/04/11 - Advanced Instruments Inc. (AI Companies) + Advanced Instruments Inc. (AI Companies) + + Karin Breuer + WEB:http://www.aicompanies.com/@2011/04/11 + Advanced Instruments Inc. (AI Companies) @@ -122789,10 +143683,11 @@ realizes some 'host of immune response role' - Miltenyi Biotec - Karin Breuer - WEB:http://www.miltenyibiotec.com/@2011/04/11 - Miltenyi Biotec + Miltenyi Biotec + + Karin Breuer + WEB:http://www.miltenyibiotec.com/@2011/04/11 + Miltenyi Biotec @@ -122801,10 +143696,11 @@ realizes some 'host of immune response role' - AES Chemunex - Karin Breuer - WEB:http://www.aeschemunex.com/@2011/04/11 - AES Chemunex + AES Chemunex + + Karin Breuer + WEB:http://www.aeschemunex.com/@2011/04/11 + AES Chemunex @@ -122813,10 +143709,11 @@ realizes some 'host of immune response role' - Bentley Instruments - Karin Breuer - WEB:http://bentleyinstruments.com/@2011/04/11 - Bentley Instruments + Bentley Instruments + + Karin Breuer + WEB:http://bentleyinstruments.com/@2011/04/11 + Bentley Instruments @@ -122825,10 +143722,11 @@ realizes some 'host of immune response role' - Invitrogen - Karin Breuer - WEB:http://www.invitrogen.com/@2011/04/11 - Invitrogen + Invitrogen + + Karin Breuer + WEB:http://www.invitrogen.com/@2011/04/11 + Invitrogen @@ -122837,10 +143735,11 @@ realizes some 'host of immune response role' - Luminex - Karin Breuer - WEB:http://www.luminexcorp.com/@2011/04/11 - Luminex + Luminex + + Karin Breuer + WEB:http://www.luminexcorp.com/@2011/04/11 + Luminex @@ -122849,10 +143748,11 @@ realizes some 'host of immune response role' - CytoBuoy - Karin Breuer - WEB:http://www.cytobuoy.com/@2011/04/11 - CytoBuoy + CytoBuoy + + Karin Breuer + WEB:http://www.cytobuoy.com/@2011/04/11 + CytoBuoy @@ -122861,10 +143761,11 @@ realizes some 'host of immune response role' - Nimblegen - An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. - Person: Jie Zheng - Nimblegen + Nimblegen + + An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. + Person: Jie Zheng + Nimblegen @@ -122873,10 +143774,11 @@ realizes some 'host of immune response role' - Pacific Biosciences - An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. - Person: Jie Zheng - Pacific Biosciences + Pacific Biosciences + + An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. + Person: Jie Zheng + Pacific Biosciences @@ -122885,9 +143787,10 @@ realizes some 'host of immune response role' - NanoString Technologies - An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. - NanoString Technologies + NanoString Technologies + + An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. + NanoString Technologies @@ -122896,11 +143799,12 @@ realizes some 'host of immune response role' - Thermo Fisher Scientific - An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific - Thermo Fisher Scientific + Thermo Fisher Scientific + + An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific + Thermo Fisher Scientific @@ -122909,12 +143813,14 @@ realizes some 'host of immune response role' - A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. - Chris Stoeckert, Helena Ellis - G1 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB - G1: Well differentiated + G1: Well differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. + Chris Stoeckert, Helena Ellis + G1 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G1: Well differentiated @@ -122923,12 +143829,14 @@ realizes some 'host of immune response role' - A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. - Chris Stoeckert, Helena Ellis - G2 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB - G2: Moderately differentiated + G2: Moderately differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. + Chris Stoeckert, Helena Ellis + G2 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G2: Moderately differentiated @@ -122937,12 +143845,14 @@ realizes some 'host of immune response role' - A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. - Chris Stoeckert, Helena Ellis - G3 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB - G3: Poorly differentiated + G3: Poorly differentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. + Chris Stoeckert, Helena Ellis + G3 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G3: Poorly differentiated @@ -122951,12 +143861,14 @@ realizes some 'host of immune response role' - A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. - Chris Stoeckert, Helena Ellis - G4 - https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet - NCI BBRB - G4: Undifferentiated + G4: Undifferentiated + + A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. + Chris Stoeckert, Helena Ellis + G4 + https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet + NCI BBRB + G4: Undifferentiated @@ -122965,12 +143877,14 @@ realizes some 'host of immune response role' - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. - Chris Stoeckert, Helena Ellis - Grade 1 - NCI BBRB, OBI - NCI BBRB - G1 (Fuhrman) + G1 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. + Chris Stoeckert, Helena Ellis + Grade 1 + NCI BBRB, OBI + NCI BBRB + G1 (Fuhrman) @@ -122979,12 +143893,14 @@ realizes some 'host of immune response role' - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. - Chris Stoeckert, Helena Ellis - Grade 2 - NCI BBRB, OBI - NCI BBRB - G2 (Fuhrman) + G2 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. + Chris Stoeckert, Helena Ellis + Grade 2 + NCI BBRB, OBI + NCI BBRB + G2 (Fuhrman) @@ -122993,12 +143909,14 @@ realizes some 'host of immune response role' - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. - Chris Stoeckert, Helena Ellis - Grade 3 - NCI BBRB, OBI - NCI BBRB - G3 (Fuhrman) + G3 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. + Chris Stoeckert, Helena Ellis + Grade 3 + NCI BBRB, OBI + NCI BBRB + G3 (Fuhrman) @@ -123007,12 +143925,14 @@ realizes some 'host of immune response role' - A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. - Chris Stoeckert, Helena Ellis - Grade 4 - NCI BBRB, OBI - NCI BBRB - G4 (Fuhrman) + G4 (Fuhrman) + + A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. + Chris Stoeckert, Helena Ellis + Grade 4 + NCI BBRB, OBI + NCI BBRB + G4 (Fuhrman) @@ -123021,12 +143941,14 @@ realizes some 'host of immune response role' - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. - Chris Stoeckert, Helena Ellis - Low grade - NCI BBRB, OBI - NCI BBRB - Low grade ovarian tumor + Low grade ovarian tumor + + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. + Chris Stoeckert, Helena Ellis + Low grade + NCI BBRB, OBI + NCI BBRB + Low grade ovarian tumor @@ -123035,12 +143957,14 @@ realizes some 'host of immune response role' - A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. - Chris Stoeckert, Helena Ellis - High grade - NCI BBRB, OBI - NCI BBRB - High grade ovarian tumor + High grade ovarian tumor + + A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. + Chris Stoeckert, Helena Ellis + High grade + NCI BBRB, OBI + NCI BBRB + High grade ovarian tumor @@ -123049,12 +143973,14 @@ realizes some 'host of immune response role' - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. - Chris Stoeckert, Helena Ellis - G1 - NCI BBRB, OBI - NCI BBRB - G1 (WHO) + G1 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. + Chris Stoeckert, Helena Ellis + G1 + NCI BBRB, OBI + NCI BBRB + G1 (WHO) @@ -123063,12 +143989,14 @@ realizes some 'host of immune response role' - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. - Chris Stoeckert, Helena Ellis - G2 - NCI BBRB, OBI - NCI BBRB - G2 (WHO) + G2 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. + Chris Stoeckert, Helena Ellis + G2 + NCI BBRB, OBI + NCI BBRB + G2 (WHO) @@ -123077,12 +144005,14 @@ realizes some 'host of immune response role' - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. - Chris Stoeckert, Helena Ellis - G3 - NCI BBRB, OBI - NCI BBRB - G3 (WHO) + G3 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. + Chris Stoeckert, Helena Ellis + G3 + NCI BBRB, OBI + NCI BBRB + G3 (WHO) @@ -123091,12 +144021,14 @@ realizes some 'host of immune response role' - A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. - Chris Stoeckert, Helena Ellis - G4 - NCI BBRB, OBI - NCI BBRB - G4 (WHO) + G4 (WHO) + + A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. + Chris Stoeckert, Helena Ellis + G4 + NCI BBRB, OBI + NCI BBRB + G4 (WHO) @@ -123105,11 +144037,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT0 (colon) + pT0 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT0 (colon) @@ -123118,11 +144052,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pTis (colon) + pTis (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pTis (colon) @@ -123131,11 +144067,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT1 (colon) + pT1 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT1 (colon) @@ -123144,11 +144082,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT2 (colon) + pT2 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT2 (colon) @@ -123157,11 +144097,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT3 (colon) + pT3 (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT3 (colon) @@ -123170,11 +144112,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT4a (colon) + pT4a (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT4a (colon) @@ -123183,11 +144127,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ - NCI BBRB - pT4b (colon) + pT4b (colon) + + A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ + NCI BBRB + pT4b (colon) @@ -123196,11 +144142,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT0 (lung) + pT0 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT0 (lung) @@ -123209,11 +144157,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pTis (lung) + pTis (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pTis (lung) @@ -123222,11 +144172,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT1 (lung) + pT1 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1 (lung) @@ -123235,11 +144187,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT1a (lung) + pT1a (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1a (lung) @@ -123248,11 +144202,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT1b (lung) + pT1b (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT1b (lung) @@ -123261,11 +144217,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT2 (lung) + pT2 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2 (lung) @@ -123274,11 +144232,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT2a (lung) + pT2a (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2a (lung) @@ -123287,11 +144247,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT2b (lung) + pT2b (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT2b (lung) @@ -123300,11 +144262,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT3 (lung) + pT3 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT3 (lung) @@ -123313,11 +144277,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ - NCI BBRB - pT4 (lung) + pT4 (lung) + + A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ + NCI BBRB + pT4 (lung) @@ -123326,11 +144292,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT0 (kidney) + pT0 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT0 (kidney) @@ -123339,11 +144307,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT1 (kidney) + pT1 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1 (kidney) @@ -123352,11 +144322,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT1a (kidney) + pT1a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1a (kidney) @@ -123365,11 +144337,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT1b (kidney) + pT1b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT1b (kidney) @@ -123378,11 +144352,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT2 (kidney) + pT2 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2 (kidney) @@ -123391,11 +144367,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT2a (kidney) + pT2a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2a (kidney) @@ -123404,11 +144382,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT2b (kidney) + pT2b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT2b (kidney) @@ -123417,11 +144397,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT3 (kidney) + pT3 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3 (kidney) @@ -123430,11 +144412,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT3a (kidney) + pT3a (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3a (kidney) @@ -123443,11 +144427,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT3b (kidney) + pT3b (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3b (kidney) @@ -123456,11 +144442,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT3c (kidney) + pT3c (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT3c (kidney) @@ -123469,11 +144457,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ - NCI BBRB - pT4 (kidney) + pT4 (kidney) + + A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ + NCI BBRB + pT4 (kidney) @@ -123482,11 +144472,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT0 (ovary) + pT0 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT0 (ovary) @@ -123495,11 +144487,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT1 (ovary) + pT1 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1 (ovary) @@ -123508,11 +144502,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT1a (ovary) + pT1a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1a (ovary) @@ -123521,11 +144517,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT1b (ovary) + pT1b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1b (ovary) @@ -123534,11 +144532,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT1c (ovary) + pT1c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT1c (ovary) @@ -123547,11 +144547,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT2 (ovary) + pT2 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2 (ovary) @@ -123560,11 +144562,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT2a (ovary) + pT2a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2a (ovary) @@ -123573,11 +144577,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT2b (ovary) + pT2b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2b (ovary) @@ -123586,11 +144592,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT2c (ovary) + pT2c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT2c (ovary) @@ -123599,11 +144607,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT3 (ovary) + pT3 (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3 (ovary) @@ -123612,11 +144622,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT3a (ovary) + pT3a (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3a (ovary) @@ -123625,11 +144637,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT3b (ovary) + pT3b (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3b (ovary) @@ -123638,11 +144652,13 @@ realizes some 'host of immune response role' - A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ - NCI BBRB - pT3c (ovary) + pT3c (ovary) + + A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ + NCI BBRB + pT3c (ovary) @@ -123651,11 +144667,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN0 (colon) + pN0 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN0 (colon) @@ -123664,11 +144682,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN1 (colon) + pN1 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1 (colon) @@ -123677,11 +144697,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN1a (colon) + pN1a (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1a (colon) @@ -123690,11 +144712,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN1b (colon) + pN1b (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1b (colon) @@ -123703,11 +144727,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN1c (colon) + pN1c (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN1c (colon) @@ -123716,11 +144742,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN2 (colon) + pN2 (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2 (colon) @@ -123729,11 +144757,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN2a (colon) + pN2a (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2a (colon) @@ -123742,11 +144772,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ - NCI BBRB - pN2b (colon) + pN2b (colon) + + A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ + NCI BBRB + pN2b (colon) @@ -123755,11 +144787,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB - pN0 (lung) + pN0 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN0 (lung) @@ -123768,11 +144802,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB - pN1 (lung) + pN1 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN1 (lung) @@ -123781,11 +144817,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB - pN2 (lung) + pN2 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN2 (lung) @@ -123794,11 +144832,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ - NCI BBRB - pN3 (lung) + pN3 (lung) + + A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ + NCI BBRB + pN3 (lung) @@ -123807,11 +144847,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ - NCI BBRB - pN0 (kidney) + pN0 (kidney) + + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ + NCI BBRB + pN0 (kidney) @@ -123820,11 +144862,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ - NCI BBRB - pN1 (kidney) + pN1 (kidney) + + A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ + NCI BBRB + pN1 (kidney) @@ -123833,11 +144877,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ - NCI BBRB - pN0 (ovary) + pN0 (ovary) + + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ + NCI BBRB + pN0 (ovary) @@ -123846,11 +144892,13 @@ realizes some 'host of immune response role' - A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ - NCI BBRB - pN1 (ovary) + pN1 (ovary) + + A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ + NCI BBRB + pN1 (ovary) @@ -123859,11 +144907,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 - NCI BBRB - cM0 (colon) + cM0 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 + NCI BBRB + cM0 (colon) @@ -123872,11 +144922,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. - Chris Stoeckert, Helena Ellis - https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 - NCI BBRB - cM1 (colon) + cM1 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. + Chris Stoeckert, Helena Ellis + https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 + NCI BBRB + cM1 (colon) @@ -123885,11 +144937,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - cM1a (colon) + cM1a (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + cM1a (colon) @@ -123898,11 +144952,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - cM1b (colon) + cM1b (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + cM1b (colon) @@ -123911,11 +144967,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - pM1 (colon) + pM1 (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1 (colon) @@ -123924,11 +144982,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - pM1a (colon) + pM1a (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1a (colon) @@ -123937,11 +144997,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ - NCI BBRB - pM1b (colon) + pM1b (colon) + + A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ + NCI BBRB + pM1b (colon) @@ -123950,11 +145012,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - cM0 (lung) + cM0 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM0 (lung) @@ -123963,11 +145027,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - cM1 (lung) + cM1 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1 (lung) @@ -123976,11 +145042,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - cM1a (lung) + cM1a (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1a (lung) @@ -123989,11 +145057,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - cM1b (lung) + cM1b (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + cM1b (lung) @@ -124002,11 +145072,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - pM1 (lung) + pM1 (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1 (lung) @@ -124015,11 +145087,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - pM1a (lung) + pM1a (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1a (lung) @@ -124028,11 +145102,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ - NCI BBRB - pM1b (lung) + pM1b (lung) + + A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ + NCI BBRB + pM1b (lung) @@ -124041,11 +145117,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB - cM0 (kidney) + cM0 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + cM0 (kidney) @@ -124054,11 +145132,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB - cM1 (kidney) + cM1 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + cM1 (kidney) @@ -124067,11 +145147,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ - NCI BBRB - pM1 (kidney) + pM1 (kidney) + + A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ + NCI BBRB + pM1 (kidney) @@ -124080,11 +145162,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB - cM0 (ovary) + cM0 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + cM0 (ovary) @@ -124093,11 +145177,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB - cM1 (ovary) + cM1 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + cM1 (ovary) @@ -124106,11 +145192,13 @@ realizes some 'host of immune response role' - A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. - Chris Stoeckert, Helena Ellis - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ - NCI BBRB - pM1 (ovary) + pM1 (ovary) + + A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. + Chris Stoeckert, Helena Ellis + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ + NCI BBRB + pM1 (ovary) @@ -124119,12 +145207,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. - Chris Stoeckert, Helena Ellis - Occult Carcinoma - http://www.medilexicon.com/dictionary/14371 - NCI BBRB - Occult Carcinoma (AJCC 7th) + Occult Carcinoma (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. + Chris Stoeckert, Helena Ellis + Occult Carcinoma + http://www.medilexicon.com/dictionary/14371 + NCI BBRB + Occult Carcinoma (AJCC 7th) @@ -124133,12 +145223,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. - Chris Stoeckert, Helena Ellis - Stage 0 - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage 0 (AJCC 7th) + Stage 0 (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. + Chris Stoeckert, Helena Ellis + Stage 0 + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage 0 (AJCC 7th) @@ -124147,12 +145239,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. - Chris Stoeckert, Helena Ellis - Stage I - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage I (AJCC 7th) + Stage I (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. + Chris Stoeckert, Helena Ellis + Stage I + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage I (AJCC 7th) @@ -124161,12 +145255,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. - Chris Stoeckert, Helena Ellis - Stage IIA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIA (AJCC 7th) + Stage IIA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. + Chris Stoeckert, Helena Ellis + Stage IIA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIA (AJCC 7th) @@ -124175,12 +145271,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. - Chris Stoeckert, Helena Ellis - Stage IIB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIB (AJCC 7th) + Stage IIB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. + Chris Stoeckert, Helena Ellis + Stage IIB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIB (AJCC 7th) @@ -124189,12 +145287,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. - Chris Stoeckert, Helena Ellis - Stage IIC - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIC (AJCC 7th) + Stage IIC (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. + Chris Stoeckert, Helena Ellis + Stage IIC + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIC (AJCC 7th) @@ -124203,12 +145303,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. - Chris Stoeckert, Helena Ellis - Stage IIIA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIIA (AJCC 7th) + Stage IIIA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. + Chris Stoeckert, Helena Ellis + Stage IIIA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIA (AJCC 7th) @@ -124217,12 +145319,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. - Chris Stoeckert, Helena Ellis - Stage IIIB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIIB (AJCC 7th) + Stage IIIB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. + Chris Stoeckert, Helena Ellis + Stage IIIB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIB (AJCC 7th) @@ -124231,12 +145335,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. - Chris Stoeckert, Helena Ellis - Stage IIIC - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IIIC (AJCC 7th) + Stage IIIC (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. + Chris Stoeckert, Helena Ellis + Stage IIIC + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IIIC (AJCC 7th) @@ -124245,12 +145351,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. - Chris Stoeckert, Helena Ellis - Stage IVA - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IVA (AJCC 7th) + Stage IVA (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. + Chris Stoeckert, Helena Ellis + Stage IVA + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IVA (AJCC 7th) @@ -124259,12 +145367,14 @@ realizes some 'host of immune response role' - A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. - Chris Stoeckert, Helena Ellis - Stage IVB - https://en.wikipedia.org/wiki/Cancer_staging - NCI BBRB - Stage IVB (AJCC 7th) + Stage IVB (AJCC 7th) + + A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. + Chris Stoeckert, Helena Ellis + Stage IVB + https://en.wikipedia.org/wiki/Cancer_staging + NCI BBRB + Stage IVB (AJCC 7th) @@ -124273,12 +145383,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. - Chris Stoeckert, Helena Ellis - Stage IA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IA (FIGO) + Stage IA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. + Chris Stoeckert, Helena Ellis + Stage IA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA (FIGO) @@ -124287,12 +145399,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. - Chris Stoeckert, Helena Ellis - Stage IA1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IA1 (FIGO) + Stage IA1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. + Chris Stoeckert, Helena Ellis + Stage IA1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA1 (FIGO) @@ -124301,12 +145415,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. - Chris Stoeckert, Helena Ellis - Stage IA2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IA2 (FIGO) + Stage IA2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. + Chris Stoeckert, Helena Ellis + Stage IA2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IA2 (FIGO) @@ -124315,12 +145431,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA - Chris Stoeckert, Helena Ellis - Stage IB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IB (FIGO) + Stage IB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA + Chris Stoeckert, Helena Ellis + Stage IB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB (FIGO) @@ -124329,12 +145447,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IB1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IB1 (FIGO) + Stage IB1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IB1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB1 (FIGO) @@ -124343,12 +145463,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IB2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IB2 (FIGO) + Stage IB2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IB2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IB2 (FIGO) @@ -124357,12 +145479,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. - Chris Stoeckert, Helena Ellis - Stage IIA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIA (FIGO) + Stage IIA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. + Chris Stoeckert, Helena Ellis + Stage IIA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA (FIGO) @@ -124371,12 +145495,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IIA1 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIA1 (FIGO) + Stage IIA1 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IIA1 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA1 (FIGO) @@ -124385,12 +145511,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. - Chris Stoeckert, Helena Ellis - Stage IIA2 - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIA2 (FIGO) + Stage IIA2 (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. + Chris Stoeckert, Helena Ellis + Stage IIA2 + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIA2 (FIGO) @@ -124399,12 +145527,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. - Chris Stoeckert, Helena Ellis - Stage IIB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIB (FIGO) + Stage IIB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. + Chris Stoeckert, Helena Ellis + Stage IIB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIB (FIGO) @@ -124413,12 +145543,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. - Chris Stoeckert, Helena Ellis - Stage IIIA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIIA (FIGO) + Stage IIIA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. + Chris Stoeckert, Helena Ellis + Stage IIIA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIIA (FIGO) @@ -124427,12 +145559,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. - Chris Stoeckert, Helena Ellis - Stage IIIB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IIIB (FIGO) + Stage IIIB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. + Chris Stoeckert, Helena Ellis + Stage IIIB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IIIB (FIGO) @@ -124441,12 +145575,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. - Chris Stoeckert, Helena Ellis - Stage IVA - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IVA (FIGO) + Stage IVA (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. + Chris Stoeckert, Helena Ellis + Stage IVA + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IVA (FIGO) @@ -124455,12 +145591,14 @@ realizes some 'host of immune response role' - An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. - Chris Stoeckert, Helena Ellis - Stage IVB - https://en.wikipedia.org/wiki/Cervical_cancer_staging - NCI BBRB - Stage IVB (FIGO) + Stage IVB (FIGO) + + An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. + Chris Stoeckert, Helena Ellis + Stage IVB + https://en.wikipedia.org/wiki/Cervical_cancer_staging + NCI BBRB + Stage IVB (FIGO) @@ -124469,12 +145607,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 1 (FIGO) + Stage 1 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1 (FIGO) @@ -124483,12 +145623,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 1A (FIGO) + Stage 1A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1A (FIGO) @@ -124497,12 +145639,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 1B (FIGO) + Stage 1B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1B (FIGO) @@ -124511,12 +145655,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 1C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 1C (FIGO) + Stage 1C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 1C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 1C (FIGO) @@ -124525,12 +145671,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 2 (FIGO) + Stage 2 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2 (FIGO) @@ -124539,12 +145687,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 2A (FIGO) + Stage 2A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2A (FIGO) @@ -124553,12 +145703,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 2B (FIGO) + Stage 2B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2B (FIGO) @@ -124567,12 +145719,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. - Chris Stoeckert, Helena Ellis - Stage 2C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 2C (FIGO) + Stage 2C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. + Chris Stoeckert, Helena Ellis + Stage 2C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 2C (FIGO) @@ -124581,12 +145735,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). - Chris Stoeckert, Helena Ellis - Stage 3 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 3 (FIGO) + Stage 3 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). + Chris Stoeckert, Helena Ellis + Stage 3 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3 (FIGO) @@ -124595,12 +145751,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . - Chris Stoeckert, Helena Ellis - Stage 3A - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 3A (FIGO) + Stage 3A (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . + Chris Stoeckert, Helena Ellis + Stage 3A + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3A (FIGO) @@ -124609,12 +145767,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . - Chris Stoeckert, Helena Ellis - Stage 3B - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 3B (FIGO) + Stage 3B (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . + Chris Stoeckert, Helena Ellis + Stage 3B + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3B (FIGO) @@ -124623,12 +145783,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). - Chris Stoeckert, Helena Ellis - Stage 3C - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 3C (FIGO) + Stage 3C (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). + Chris Stoeckert, Helena Ellis + Stage 3C + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 3C (FIGO) @@ -124637,12 +145799,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. - Chris Stoeckert, Helena Ellis - Stage 4 - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage 4 (FIGO) + Stage 4 (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. + Chris Stoeckert, Helena Ellis + Stage 4 + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage 4 (FIGO) @@ -124651,12 +145815,14 @@ realizes some 'host of immune response role' - A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). - Chris Stoeckert, Helena Ellis - Stage Unknown - https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ - NCI BBRB - Stage Unknown (FIGO) + Stage Unknown (FIGO) + + A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). + Chris Stoeckert, Helena Ellis + Stage Unknown + https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ + NCI BBRB + Stage Unknown (FIGO) @@ -124665,11 +145831,13 @@ realizes some 'host of immune response role' - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 3: symptomatic in bed more than 50% of the day but not bed ridden + 3: symptomatic in bed more than 50% of the day but not bed ridden + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 3: symptomatic in bed more than 50% of the day but not bed ridden @@ -124678,11 +145846,13 @@ realizes some 'host of immune response role' - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 2: symptomatic but in bed less than 50% of the day + 2: symptomatic but in bed less than 50% of the day + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 2: symptomatic but in bed less than 50% of the day @@ -124691,11 +145861,13 @@ realizes some 'host of immune response role' - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 4: bed ridden + 4: bed ridden + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 4: bed ridden @@ -124704,11 +145876,13 @@ realizes some 'host of immune response role' - An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 0: asymptomatic + 0: asymptomatic + + An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 0: asymptomatic @@ -124717,11 +145891,13 @@ realizes some 'host of immune response role' - An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 1: symptomatic but fully ambulatory + 1: symptomatic but fully ambulatory + + An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 1: symptomatic but fully ambulatory @@ -124730,11 +145906,13 @@ realizes some 'host of immune response role' - A Karnofsky score vaue specification indicating that a patient is asymptomatic. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 100: asymptomatic + 100: asymptomatic + + A Karnofsky score vaue specification indicating that a patient is asymptomatic. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 100: asymptomatic @@ -124743,11 +145921,13 @@ realizes some 'host of immune response role' - A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 80-90: symptomatic but fully ambulatory + 80-90: symptomatic but fully ambulatory + + A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 80-90: symptomatic but fully ambulatory @@ -124756,11 +145936,13 @@ realizes some 'host of immune response role' - A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 60-70: symptomatic but in bed less than 50% of the day + 60-70: symptomatic but in bed less than 50% of the day + + A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 60-70: symptomatic but in bed less than 50% of the day @@ -124769,11 +145951,13 @@ realizes some 'host of immune response role' - A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. - Chris Stoeckert, Helena Ellis - NCI BBRB, OBI - NCI BBRB - 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden + 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden + + A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. + Chris Stoeckert, Helena Ellis + NCI BBRB, OBI + NCI BBRB + 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden @@ -124782,11 +145966,12 @@ realizes some 'host of immune response role' - Oxford Nanopore Technologies - An organization that is developing and selling nanopore sequencing products and is based in the UK. - James A. Overton - https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies - Oxford Nanopore Technologies + Oxford Nanopore Technologies + + An organization that is developing and selling nanopore sequencing products and is based in the UK. + James A. Overton + https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies + Oxford Nanopore Technologies @@ -124795,26 +145980,264 @@ realizes some 'host of immune response role' - BioGents - An organization that manufactures mosquito traps and other mosquito control products. - John Judkins - WEB:https://eu.biogents.com/about-biogents/ - BioGents + BioGents + + An organization that manufactures mosquito traps and other mosquito control products. + John Judkins + WEB:https://eu.biogents.com/about-biogents/ + BioGents + + + + + + + + + +## Elucidation + +This is used when the statement/axiom is assumed to hold true 'eternally' + +## How to interpret (informal) + +First the "atemporal" FOL is derived from the OWL using the standard +interpretation. This axiom is temporalized by embedding the axiom +within a for-all-times quantified sentence. The t argument is added to +all instantiation predicates and predicates that use this relation. + +## Example + + Class: nucleus + SubClassOf: part_of some cell + + forall t : + forall n : + instance_of(n,Nucleus,t) + implies + exists c : + instance_of(c,Cell,t) + part_of(n,c,t) + +## Notes + +This interpretation is *not* the same as an at-all-times relation + + + axiom holds for all times + + + + + + + + + +## Elucidation + +This is used when the first-order logic form of the relation is +binary, and takes no temporal argument. + +## Example: + + Class: limb + SubClassOf: develops_from some lateral-plate-mesoderm + + forall t, t2: + forall x : + instance_of(x,Limb,t) + implies + exists y : + instance_of(y,LPM,t2) + develops_from(x,y) + + + + relation has no temporal argument + + + + + + + + + meter + A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. + m + + meter + + + + + + + + + kilogram + A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. + kg + + kilogram + + + + + + + + + second + A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. + s + sec + + second + + + + + + + + + centimeter + A length unit which is equal to one hundredth of a meter or 10^[-2] m. + cm + + centimeter + + + + + + + + + millimeter + A length unit which is equal to one thousandth of a meter or 10^[-3] m. + mm + + millimeter + + + + + + + + + micrometer + A length unit which is equal to one millionth of a meter or 10^[-6] m. + um + + micrometer + + + + + + + + + nanometer + A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. + nm + + nanometer - + + + angstrom + A length unit which is equal to 10 [-10] m. + + angstrom + + + + + + + + + gram + A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. + g + + gram + + + + + + + + + milligram + A mass unit which is equal to one thousandth of a gram or 10^[-3] g. + mg + + milligram + + + + + + + + + microgram + A mass unit which is equal to one millionth of a gram or 10^[-6] g. + ug + + microgram + + + + + + + + + nanogram + A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. + ng + + nanogram + + + + + + + + + picogram + A mass unit which is equal to 10^[-12] g. + pg + + picogram + - C - degree C + + degree Celsius + A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. + C + degree C + + degree Celsius @@ -124822,7 +146245,152 @@ realizes some 'host of immune response role' - min + + minute + A time unit which is equal to 60 seconds. + min + + minute + + + + + + + + + hour + A time unit which is equal to 3600 seconds or 60 minutes. + h + hr + + hour + + + + + + + + + day + A time unit which is equal to 24 hours. + + day + + + + + + + + + week + A time unit which is equal to 7 days. + + week + + + + + + + + + month + A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. + + month + + + + + + + + + year + A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. + + year + + + + + + + + + micromole + A substance unit equal to a millionth of a mol or 10^[-6] mol. + umol + + micromole + + + + + + + + + nanomole + A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. + nmol + + nanomole + + + + + + + + + picomole + A substance unit equal to 10^[-12] mol. + pmol + + picomole + + + + + + + + + molar + A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). + M + + molar + + + + + + + + + millimolar + A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. + mM + + millimolar + + + + + + + + + micromolar + A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. + uM + + micromolar @@ -124830,41 +146398,347 @@ realizes some 'host of immune response role' - nM + + nanomolar + A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. + nM + + nanomolar + + + + + + + + + picomolar + A unit of molarity which is equal to 10^[-12] M. + pM + + picomolar + + + + + + + + + cubic centimeter + A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. + cc + + cubic centimeter + + + + + + + + + milliliter + A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. + ml + + milliliter + + + + + + + + + liter + A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. + L + + liter + + + + + + + + + cubic decimeter + A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. + + cubic decimeter + + + + + + + + + microliter + A volume unit which is equal to one millionth of a liter or 10^[-6] L. + ul + + microliter + + + + + + + + + nanoliter + A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. + nl + + nanoliter + + + + + + + + + picoliter + A volume unit which is equal to 10^[-12] L. + pl + + picoliter - + + + hertz + A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. + + hertz + + + + + + + + + mass percentage + A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. + % w/w + percent weight pr weight + + mass percentage + + + + + + + + + mass volume percentage + A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. + % w/v + percent vol per vol + + mass volume percentage + + + + + + + + + volume percentage + A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. + % v/v + percent vol per vol + + volume percentage + + + + + + + + + gram per liter + A mass unit density which is equal to mass of an object in grams divided by the volume in liters. + g per L + g/L + + gram per liter + + + + + + + + + milligram per milliliter + A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. + mg per ml + mg/ml + + milligram per milliliter + + + + + + + + + degree Fahrenheit + A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. + + degree Fahrenheit + + + + + + + + + pH + A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). + + pH + + + + + + + + + milliliter per liter + A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. + ml per L + ml/l + + milliliter per liter + + + + + + + + + gram per deciliter + A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. + g/dl + + gram per deciliter + + + + + + + + + colony forming unit per volume + A concentration unit which a measure of viable bacterial numbers in a given volume. + + colony forming unit per volume + + + + + + + + + microliters per minute + A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. + + microliters per minute + - + + + count per nanomolar second + A rate unit which is equal to one over one nanomolar second. + + count per nanomolar second + - + + + count per molar second + A rate unit which is equal to one over one molar second. + + count per molar second + - + + + count per nanomolar + A rate unit which is equal to one over one nanomolar. + + count per nanomolar + - - - 2 - + + + count per molar + A rate unit which is equal to one over one molar. + + count per molar + + + + + + + + + microgram per liter + A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. + ng/ml + ug/L + + microgram per liter + + + + + + + + + + + + + @@ -124876,116 +146750,104 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - m - - - kg - - - s - sec - - - cm - - - mm - - - um - - - nm - - - g - - - mg - - - ug - - - ng - - - pg - - - h - hr - - - umol + + Person:Alan Ruttenberg - - nmol + + To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) + To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - pmol - - - M - - - mM - - - uM - - - pM - - - cc - - - ml - - - L - - - ul - - - nl - - - pl - - - % w/w - percent weight pr weight + + + + To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) + + + + + + To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) + + + + A reference to a place on the Earth, by its name or by its geographical location. + geographic location + - - % w/v - percent vol per vol + + + + + + + + + + + + - - % v/v - percent vol per vol + + + + + + + - - g per L - g/L + + + + + + + + - - mg per ml - mg/ml + + + + + + + + - - ml/l - ml per L + + + + + + + - - g/dl + + + + + + + + + + + + - - ug/L - ng/ml + + + + + + + + diff --git a/views/obi.obo b/views/obi.obo index 3ee9a31f..fd990a5a 100644 --- a/views/obi.obo +++ b/views/obi.obo @@ -1,8 +1,8 @@ format-version: 1.2 -data-version: obi/2022-07-11/obi.obo -date: 11:07:2022 15:37 +data-version: 2022-12-14 +date: 14:12:2022 09:26 remark: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. -ontology: obi.obo +ontology: obi property_value: defaultLanguage "en" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Alan Ruttenberg" xsd:string @@ -67,7 +67,7 @@ property_value: http://purl.org/dc/elements/1.1/subject "An ontology for the ann property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ xsd:string property_value: http://purl.org/dc/terms/title "Ontology for Biomedical Investigations" xsd:string property_value: IAO:0000589 "Ontology for Biomedical Investigations" xsd:string -property_value: owl:versionInfo "2022-07-11" xsd:string +property_value: owl:versionInfo "2022-12-14" xsd:string [Term] id: APOLLO_SV:00000008 @@ -1102,6 +1102,7 @@ is_a: CL:0000000 ! cell [Term] id: CL:0000236 name: B cell +def: "A lymphocyte of B lineage that is capable of B cell mediated immunity." [] is_a: CL:0000542 ! lymphocyte [Term] @@ -1242,6 +1243,12 @@ name: mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [] is_a: CL:0000000 ! cell +[Term] +id: CL:0001064 +name: malignant cell +def: "A neoplastic cell that is capable of entering a surrounding tissue" [] +is_a: CL:0000000 ! cell + [Term] id: CL:0002192 name: metamyelocyte @@ -1266,6 +1273,13 @@ name: segmented neutrophil of bone marrow def: "A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface." [] is_a: CL:0000775 ! neutrophil +[Term] +id: CL:2000001 +name: peripheral blood mononuclear cell +def: "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood." [] +is_a: CL:0000003 ! native cell +is_a: CL:0000842 ! mononuclear cell + [Term] id: CLO:0000001 name: cell line cell @@ -1347,8 +1361,8 @@ is_a: OBI:0001588 ! binding [Term] id: GO:0001172 -name: transcription, RNA-templated -def: "The cellular synthesis of RNA on a template of RNA." [] +name: RNA-templated transcription +def: "The synthesis of an RNA transcript from an RNA template." [] is_a: GO:0009987 ! cellular process [Term] @@ -1457,6 +1471,12 @@ name: catalytic activity def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [] is_a: GO:0003674 ! molecular_function +[Term] +id: GO:0003939 +name: L-iditol 2-dehydrogenase activity +def: "Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+." [] +is_a: GO:0003824 ! catalytic activity + [Term] id: GO:0003964 name: RNA-directed DNA polymerase activity @@ -1469,12 +1489,72 @@ name: acetylcholinesterase activity def: "Catalysis of the reaction: acetylcholine + H2O = choline + acetate." [] is_a: GO:0003824 ! catalytic activity +[Term] +id: GO:0003997 +name: acyl-CoA oxidase activity +def: "Catalysis of the reaction: acyl-CoA + O2 = trans-2,3-dehydroacyl-CoA + hydrogen peroxide." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0004021 +name: L-alanine:2-oxoglutarate aminotransferase activity +def: "Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0004035 +name: alkaline phosphatase activity +def: "Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0004069 +name: L-aspartate:2-oxoglutarate aminotransferase activity +def: "Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0004104 +name: cholinesterase activity +def: "Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0004111 +name: creatine kinase activity +def: "Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+)." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0004353 +name: glutamate dehydrogenase [NAD(P)+] activity +def: "Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+." [] +is_a: GO:0003824 ! catalytic activity + [Term] id: GO:0004364 name: glutathione transferase activity def: "Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group." [] is_a: GO:0003824 ! catalytic activity +[Term] +id: GO:0004448 +name: isocitrate dehydrogenase [NAD(P)+] activity +def: "Catalysis of the reaction: isocitrate + NAD(P)+ = 2-oxoglutarate + CO2 + NAD(P)H." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0004457 +name: lactate dehydrogenase activity +def: "Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0004540 +name: ribonuclease activity +def: "Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA." [] +is_a: GO:0003824 ! catalytic activity + [Term] id: GO:0005216 name: ion channel activity @@ -1572,6 +1652,12 @@ name: opsonization def: "The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody." [] is_a: GO:0006909 ! phagocytosis +[Term] +id: GO:0008253 +name: 5'-nucleotidase activity +def: "Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate." [] +is_a: GO:0003824 ! catalytic activity + [Term] id: GO:0008283 name: cell population proliferation @@ -1602,12 +1688,30 @@ name: vascular endothelial growth factor production def: "The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production +[Term] +id: GO:0015925 +name: galactosidase activity +def: "Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative." [] +is_a: GO:0003824 ! catalytic activity + [Term] id: GO:0016064 name: immunoglobulin mediated immune response def: "An immune response mediated by immunoglobulins, whether cell-bound or in solution." [] is_a: GO:0008150 ! biological_process +[Term] +id: GO:0016160 +name: amylase activity +def: "Catalysis of the hydrolysis of amylose or an amylose derivative." [] +is_a: GO:0003824 ! catalytic activity + +[Term] +id: GO:0016231 +name: beta-N-acetylglucosaminidase activity +def: "Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides." [] +is_a: GO:0003824 ! catalytic activity + [Term] id: GO:0016570 name: histone modification @@ -2076,6 +2180,12 @@ name: chemokine (C-C motif) ligand 17 production def: "The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production +[Term] +id: GO:0047823 +name: D-glutamyltransferase activity +def: "Catalysis of the reaction: L(or D)-glutamine + D-glutamyl-peptide = NH3 + 5-glutamyl-D-glutamyl-peptide." [] +is_a: GO:0003824 ! catalytic activity + [Term] id: GO:0048869 name: cellular developmental process @@ -3753,10 +3863,17 @@ id: NCBITaxon:33154 name: Opisthokonta is_a: NCBITaxon:2759 ! Eukaryota +[Term] +id: NCBITaxon:33208 +name: Metazoa +synonym: "metazoans" EXACT [] +synonym: "multicellular animals" EXACT [] +is_a: NCBITaxon:33154 ! Opisthokonta + [Term] id: NCBITaxon:33213 name: Bilateria -is_a: NCBITaxon:33154 ! Opisthokonta +is_a: NCBITaxon:33208 ! Metazoa [Term] id: NCBITaxon:3702 @@ -3821,7 +3938,6 @@ is_a: NCBITaxon:2759 ! Eukaryota [Term] id: NCBITaxon:6239 name: Caenorhabditis elegans -synonym: "roundworm" EXACT [] is_a: NCBITaxon:1206794 ! Ecdysozoa [Term] @@ -3895,7 +4011,6 @@ id: NCBITaxon:9606 name: Homo sapiens synonym: "human" EXACT [] synonym: "human being" EXACT [] -synonym: "man" EXACT [] is_a: NCBITaxon:314146 ! Euarchontoglires [Term] @@ -5426,8 +5541,8 @@ is_obsolete: true [Term] id: OBI:0000447 -name: intra cellular electrophysiology recording assay -def: "An electrophysiology recording assay where the recording location of the electrode is intracellular" [] +name: intracellular electrophysiology recording assay +def: "An electrophysiology assay where the recording location of the electrode is intracellular." [] is_a: OBI:0002176 ! electrophysiology assay [Term] @@ -5464,7 +5579,7 @@ is_a: BFO:0000034 ! function [Term] id: OBI:0000454 name: extracellular electrophysiology recording assay -def: "An electrophysiology recording assay where the recording location of the electrode is extracellular" [] +def: "An electrophysiology assay where the recording location of the electrode is extracellular." [] is_a: OBI:0002176 ! electrophysiology assay [Term] @@ -6970,8 +7085,8 @@ is_a: OBI:0000094 ! material processing [Term] id: OBI:0000712 name: pathogen challenge -def: "A pathogen challenge is the administration of a live pathogenic organism to a host" [] -is_a: OBI:0600007 ! administering substance in vivo +def: "The administration of a live pathogenic organism to a host." [] +is_a: OBI:0003456 ! in vivo challenge [Term] id: OBI:0000713 @@ -7269,9 +7384,10 @@ is_a: OBI:0000822 ! single blind study execution [Term] id: OBI:0000794 -name: transcription factor binding site -comment: PLace_holder for sequence ontology term -is_a: OBI:0000905 ! sequence feature annotation +name: obsolete transcription factor binding site +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true +replaced_by: SO:0000235 [Term] id: OBI:0000795 @@ -7608,7 +7724,7 @@ is_obsolete: true [Term] id: OBI:0000852 name: record of missing knowledge -def: "a information content entity created to indicate that information about something is not available to the person recording it." [] +def: "An information content entity created to indicate that information about something is not available to the person recording it." [] is_a: IAO:0000030 ! information content entity [Term] @@ -9563,7 +9679,7 @@ is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001178 name: efficacy of epitope intervention experiment -def: "An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism. " [] +def: "An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism. " [] synonym: "efficacy of in vivo intervention" EXACT [] is_a: OBI:0000070 ! assay @@ -9596,7 +9712,7 @@ is_a: OBI:0003141 ! categorical binding datum id: OBI:0001183 name: epitope protection from tumor challenge experiment def: "An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. " [] -synonym: "tumor burden after challenge" EXACT [] +synonym: "protection from tumor challenge" EXACT [] is_a: OBI:0001184 ! epitope protection experiment [Term] @@ -9619,7 +9735,7 @@ is_a: OBI:0100026 ! organism id: OBI:0001186 name: epitope protection from infectious challenge experiment based on pathogen burden def: "An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. " [] -synonym: "pathogen urden after infectious challenge" EXACT [] +synonym: "burden after infectious challenge" EXACT [] is_a: OBI:0001179 ! epitope protection from infectious challenge experiment [Term] @@ -9889,10 +10005,10 @@ is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001228 -name: biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response +name: in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response def: "A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response." [] -synonym: "antibody help|biological activity" EXACT [] -is_a: OBI:0001495 ! biological activity assay measuring epitope specific T cell helper activity +synonym: "antibody help|in vivo assay" EXACT [] +is_a: OBI:0001495 ! in vivo assay measuring epitope specific T cell helper activity [Term] id: OBI:0001229 @@ -9990,10 +10106,10 @@ is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by [Term] id: OBI:0001242 -name: detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor production by T cells -def: "A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor production by T cells." [] +name: detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells +def: "A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|RNA/DNA detection" EXACT [] -is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells is_a: OBI:0001788 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] @@ -10143,10 +10259,10 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001263 -name: biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response +name: in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response def: "A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response." [] -synonym: "T cell help|biological activity" EXACT [] -is_a: OBI:0001495 ! biological activity assay measuring epitope specific T cell helper activity +synonym: "T cell help|in vivo assay" EXACT [] +is_a: OBI:0001495 ! in vivo assay measuring epitope specific T cell helper activity [Term] id: OBI:0001264 @@ -10555,7 +10671,8 @@ id: OBI:0001324 name: in vivo assay measuring T cell epitope specific tolerance induction def: "An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment." [] synonym: "tolerance|in vivo assay" EXACT [] -is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific in vivo activity +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity +is_a: OBI:0001488 ! epitope tolerance induction experiment [Term] id: OBI:0001325 @@ -10704,7 +10821,8 @@ id: OBI:0001348 name: in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity def: "An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity." [] synonym: "type IV hypersensitivity (DTH)|in vivo skin test" EXACT [] -is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific in vivo activity +is_a: OBI:0001178 ! efficacy of epitope intervention experiment +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0001349 @@ -10737,11 +10855,11 @@ is_a: OBI:0001364 ! genetic alteration information [Term] id: OBI:0001353 -name: cytometric bead array assay measuring epitope specific tumor necrosis factor production by T cells -def: "A cytometric bead array assay that detects tumor necrosis factor production by T cells." [] +name: cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells +def: "A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|cytometric bead array" EXACT [] is_a: OBI:0001368 ! cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells [Term] id: OBI:0001354 @@ -10999,9 +11117,11 @@ is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T ce [Term] id: OBI:0001392 name: in vivo assay measuring epitope specific T cell killing -def: "A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay." [] +def: "An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|in vivo assay" EXACT [] -is_a: OBI:1110130 ! biological activity assay measuring epitope specific T cell killing +is_a: OBI:0000883 ! in vivo cell killing assay +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity +is_a: OBI:1110130 ! assay measuring epitope specific T cell killing [Term] id: OBI:0001393 @@ -11103,7 +11223,7 @@ is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T ce [Term] id: OBI:0001407 -name: biological activity assay measuring epitope specific T cell activation +name: assay measuring epitope specific T cell activation def: "A T cell epitope dependent biological activity assay that detects T cell activation." [] synonym: "activation|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding @@ -11164,8 +11284,8 @@ is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001416 -name: assay measuring epitope specific tumor necrosis factor production by T cells -def: "An assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells that detects tumor necrosis factor production." [] +name: assay measuring epitope specific tumor necrosis factor alpha production by T cells +def: "An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production." [] synonym: "TNFa release|biological activity" EXACT [] is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells @@ -11369,11 +11489,11 @@ is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T ce [Term] id: OBI:0001452 -name: cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor production by T cells -def: "A reporter cell line analyte detection bioassay that detects tumor necrosis factor production by T cells." [] +name: cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells +def: "A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|bioassay" EXACT [] -is_a: OBI:0000904 ! reporter cell line analyte detection bioassay -is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells +is_a: OBI:0003488 ! cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001453 @@ -11473,7 +11593,8 @@ id: OBI:0001467 name: in vivo assay measuring T cell epitope specific disease exacerbation def: "An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment." [] synonym: "disease exacerbation|in vivo assay" EXACT [] -is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific in vivo activity +is_a: OBI:0001188 ! epitope disease exacerbation experiment +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0001468 @@ -11509,10 +11630,11 @@ is_a: OBI:0100051 ! specimen [Term] id: OBI:0001473 -name: in vivo assay measuring T cell epitope specific protection from tumor challenge -def: "A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden." [] +name: in vivo assay measuring T cell epitope specific protection after tumor burden challenge +def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden." [] synonym: "tumor burden after challenge|in vivo assay" EXACT [] -is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge +is_a: OBI:0003458 ! epitope protection from tumor challenge experiment based on burden +is_a: OBI:0003461 ! in vivo assay measuring T cell epitope specific protection from tumor challenge [Term] id: OBI:0001474 @@ -11523,9 +11645,10 @@ is_a: OBI:0001477 ! lowess transformation [Term] id: OBI:0001475 name: in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden -def: "A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden." [] +def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden." [] synonym: "pathogen burden after challenge|in vivo assay" EXACT [] -is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge +is_a: OBI:0001186 ! epitope protection from infectious challenge experiment based on pathogen burden +is_a: OBI:0003460 ! in vivo assay measuring T cell epitope specific protection from pathogen challenge [Term] id: OBI:0001476 @@ -11581,7 +11704,7 @@ is_a: OBI:0600014 ! material component separation [Term] id: OBI:0001484 -name: biological activity assay measuring T cell epitope specific in vivo activity +name: assay measuring T cell epitope specific in vivo activity def: "A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment." [] synonym: "in vivo activity|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding @@ -11636,9 +11759,10 @@ is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001492 name: in vivo assay measuring T cell epitope specific protection based on survival -def: "A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival." [] +def: "An in vivo assay measuring T cell epitope specific protection from other challenge using survival." [] synonym: "survival from challenge|in vivo assay" EXACT [] -is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge +is_a: OBI:0001189 ! epitope protection experiment based on survival +is_a: OBI:0003462 ! in vivo assay measuring T cell epitope specific protection from other challenge [Term] id: OBI:0001493 @@ -11655,10 +11779,10 @@ is_a: OBI:0600058 ! enzymatic amplification [Term] id: OBI:0001495 -name: biological activity assay measuring epitope specific T cell helper activity +name: in vivo assay measuring epitope specific T cell helper activity def: "A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function." [] -synonym: "helper response|biological activity" EXACT [] -is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding +synonym: "helper response|in vivo assay" EXACT [] +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0001496 @@ -11735,7 +11859,8 @@ id: OBI:0001507 name: in vivo assay measuring T cell epitope specific treatment of disease def: "An efficacy of T cell epitope intervention experiment that detects a decrease in disease." [] synonym: "decreased disease|in vivo assay" EXACT [] -is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific in vivo activity +is_a: OBI:0001190 ! epitope treatment experiment +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0001508 @@ -12681,45 +12806,45 @@ is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell e [Term] id: OBI:0001639 -name: biological activity assay measuring epitope specific Ig-mediated histamine release -def: "A B cell epitope specific activation of additional immune response in vitro assay that detects histamine release." [] +name: assay measuring epitope specific Ig-mediated histamine release +def: "A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro." [] synonym: "histamine release|biological activity" EXACT [] -is_a: OBI:0001704 ! biological activity assay measuring epitope specific activation of additional immune response in vitro +is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001640 -name: biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation +name: assay measuring epitope specific immunoglobulin-mediated antigen activation def: "A B cell epitope dependent biological activity determination assay that detects antigen activation." [] synonym: "antigen activation|biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001641 -name: biological activity assay measuring epitope specific complement-dependent cytotoxicity -def: "A B cell epitope specific activation of additional immune response in vitro assay that detects complement-dependent cytotoxicity." [] +name: assay measuring epitope specific complement-dependent cytotoxicity +def: "A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro ." [] synonym: "complement-dependent cytotoxicity|biological activity" EXACT [] -is_a: OBI:0001704 ! biological activity assay measuring epitope specific activation of additional immune response in vitro +is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001642 -name: biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity -def: "A B cell epitope specific activation of additional immune response in vitro assay that detects antibody-dependent cellular cytotoxicity." [] +name: assay measuring epitope specific antibody-dependent cellular cytotoxicity +def: "A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro." [] synonym: "antibody-dependent cellular cytotoxicity|biological activity" EXACT [] -is_a: OBI:0001704 ! biological activity assay measuring epitope specific activation of additional immune response in vitro +is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001643 -name: biological activity assay measuring epitope specific immunoglobulin-mediated neutralization +name: assay measuring epitope specific immunoglobulin-mediated neutralization def: "A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen." [] synonym: "neutralization |biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001644 -name: biological activity assay measuring epitope specific opsonization -def: "A B cell epitope specific activation of additional immune response in vitro assay that detects opsonization." [] +name: assay measuring epitope specific opsonization +def: "A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro ." [] synonym: "opsonization|biological activity" EXACT [] -is_a: OBI:0001704 ! biological activity assay measuring epitope specific activation of additional immune response in vitro +is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001645 @@ -13071,46 +13196,51 @@ id: OBI:0001692 name: in vivo assay measuring B cell epitope specific protection from fertility def: "An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility." [] synonym: "protection from fertility|in vivo assay" EXACT [] -is_a: OBI:0001698 ! biological activity assay measuring B cell epitope specific in vivo activity +is_a: OBI:0001178 ! efficacy of epitope intervention experiment +is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001693 name: in vivo assay measuring B cell epitope specific tolerance induction def: "An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment." [] synonym: "tolerance|in vivo assay" EXACT [] -is_a: OBI:0001698 ! biological activity assay measuring B cell epitope specific in vivo activity +is_a: OBI:0001488 ! epitope tolerance induction experiment +is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001694 name: in vivo assay measuring B cell epitope specific induction of hypersensitivity def: "An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions." [] synonym: "hypersensitivity|in vivo assay" EXACT [] -is_a: OBI:0001698 ! biological activity assay measuring B cell epitope specific in vivo activity +is_a: OBI:0001178 ! efficacy of epitope intervention experiment +is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001695 -name: biological activity assay measuring epitope specific immune complex formation -def: "A B cell epitope specific activation of additional immune response in vitro assay that detects agglutination." [] +name: assay measuring epitope specific immune complex formation +def: "A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro." [] synonym: "agglutination|biological activity" EXACT [] -is_a: OBI:0001704 ! biological activity assay measuring epitope specific activation of additional immune response in vitro +is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001696 name: in vivo assay measuring B cell epitope specific protection based on survival -def: "A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival." [] +def: "An in vivo assay measuring B cell epitope specific protection from other challenge using survival." [] synonym: "survival from challenge|in vivo assay" EXACT [] -is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge +is_a: OBI:0001189 ! epitope protection experiment based on survival +is_a: OBI:0003467 ! in vivo assay measuring B cell epitope specific protection from other challenge [Term] id: OBI:0001697 name: in vivo assay measuring B cell epitope specific treatment of disease def: "An efficacy of B cell epitope intervention experiment that detects a decrease in disease." [] synonym: "decreased disease|in vivo assay" EXACT [] -is_a: OBI:0001698 ! biological activity assay measuring B cell epitope specific in vivo activity +is_a: OBI:0001190 ! epitope treatment experiment +is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001698 -name: biological activity assay measuring B cell epitope specific in vivo activity +name: assay measuring B cell epitope specific in vivo activity def: "A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment." [] synonym: "in vivo activity|biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding @@ -13151,14 +13281,14 @@ is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex [Term] id: OBI:0001704 -name: biological activity assay measuring epitope specific activation of additional immune response in vitro +name: assay measuring epitope specific activation of additional immune response in vitro def: "A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity." [] synonym: "secondary in vitro activity|biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001705 -name: biological activity assay measuring epitope specific antigen inhibition of antibody activity +name: assay measuring epitope specific antigen inhibition of antibody activity def: "A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen." [] synonym: "antibody activity inhibition|biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding @@ -13195,14 +13325,16 @@ id: OBI:0001710 name: in vivo assay measuring B cell epitope specific protection from challenge def: "An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment." [] synonym: "protection from challenge|in vivo assay" EXACT [] -is_a: OBI:0001698 ! biological activity assay measuring B cell epitope specific in vivo activity +is_a: OBI:0001184 ! epitope protection experiment +is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001711 name: in vivo assay measuring B cell epitope specific disease exacerbation def: "An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment." [] synonym: "disease exacerbation|in vivo assay" EXACT [] -is_a: OBI:0001698 ! biological activity assay measuring B cell epitope specific in vivo activity +is_a: OBI:0001188 ! epitope disease exacerbation experiment +is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001712 @@ -14323,7 +14455,7 @@ name: formaldehyde-assisted isolation of regulatory elements assay def: "An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity." [] synonym: "FAIRE-seq" EXACT [] synonym: "FAIRE-seq assay" EXACT [] -is_a: OBI:0000626 ! DNA sequencing assay +is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001861 @@ -15636,16 +15768,18 @@ is_a: OBI:0002075 ! MHC ligand assay [Term] id: OBI:0002051 name: in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden -def: "A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden." [] +def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden." [] synonym: "pathogen burden after challenge|in vivo assay" EXACT [] -is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge +is_a: OBI:0001186 ! epitope protection from infectious challenge experiment based on pathogen burden +is_a: OBI:0003465 ! in vivo assay measuring B cell epitope specific protection from pathogen challenge [Term] id: OBI:0002052 -name: in vivo assay measuring B cell epitope specific protection from tumor challenge -def: "A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden." [] +name: in vivo assay measuring B cell epitope specific protection after tumor burden challenge +def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden." [] synonym: "tumor burden after challenge|in vivo assay" EXACT [] -is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge +is_a: OBI:0003458 ! epitope protection from tumor challenge experiment based on burden +is_a: OBI:0003466 ! in vivo assay measuring B cell epitope specific protection from tumor challenge [Term] id: OBI:0002053 @@ -15716,9 +15850,10 @@ is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002062 name: in vitro assay measuring epitope specific T cell killing -def: "A T cell epitope specific killing assay that uses an in vitro cell killing assay." [] +def: "An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|in vitro assay" EXACT [] -is_a: OBI:1110130 ! biological activity assay measuring epitope specific T cell killing +is_a: OBI:0000903 ! in vitro cell killing assay +is_a: OBI:1110130 ! assay measuring epitope specific T cell killing [Term] id: OBI:0002063 @@ -15781,15 +15916,15 @@ id: OBI:0002070 name: in vivo assay measuring epitope specific proliferation of T cells def: "A T cell epitope specific proliferation assay that is performed in vivo." [] synonym: "proliferation|in vivo assay" EXACT [] -is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific in vivo activity -is_a: OBI:1110131 ! biological activity assay measuring epitope specific proliferation of T cells +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity +is_a: OBI:1110131 ! assay measuring epitope specific proliferation of T cells [Term] id: OBI:0002071 name: in vitro assay measuring epitope specific proliferation of T cells def: "A T cell epitope specific proliferation assay that is performed on cells in vitro." [] synonym: "proliferation|in vitro assay" EXACT [] -is_a: OBI:1110131 ! biological activity assay measuring epitope specific proliferation of T cells +is_a: OBI:1110131 ! assay measuring epitope specific proliferation of T cells [Term] id: OBI:0002072 @@ -15803,11 +15938,12 @@ id: OBI:0002073 name: in vivo assay measuring T cell epitope specific protection from challenge def: "An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment." [] synonym: "protection from challenge|in vivo assay" EXACT [] -is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific in vivo activity +is_a: OBI:0001184 ! epitope protection experiment +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0002074 -name: in vitro assay measuring T cell epitope specific suppression +name: assay measuring T cell epitope specific suppression in vitro def: "T cell epitope dependent biological activity assay that detects suppression of an in vitro response." [] synonym: "suppression|in vitro assay" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding @@ -15958,9 +16094,10 @@ is_a: OBI:0000094 ! material processing [Term] id: OBI:0002096 name: carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells -def: "A T cell epitope specific proliferation assay performed on cells in vitro that uses a CFSE assay." [] +def: "A CFSE assay that detects T cell epitope specific proliferation in vitro." [] synonym: "proliferation|CFSE" EXACT [] is_a: OBI:0002071 ! in vitro assay measuring epitope specific proliferation of T cells +is_a: OBI:0002106 ! carboxyfluorescein succinimidyl ester staining assay [Term] id: OBI:0002097 @@ -16511,7 +16648,7 @@ is_a: OBI:0000070 ! assay id: OBI:0002177 name: patch clamp assay def: "An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations." [] -is_a: OBI:0000447 ! intra cellular electrophysiology recording assay +is_a: OBI:0000447 ! intracellular electrophysiology recording assay [Term] id: OBI:0002178 @@ -16541,7 +16678,7 @@ is_a: OBI:0002177 ! patch clamp assay id: OBI:0002182 name: voltage clamp assay def: "An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell." [] -is_a: OBI:0000447 ! intra cellular electrophysiology recording assay +is_a: OBI:0000447 ! intracellular electrophysiology recording assay [Term] id: OBI:0002183 @@ -16561,7 +16698,7 @@ is_a: OBI:0002182 ! voltage clamp assay id: OBI:0002185 name: current clamp assay def: "The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in \"current clamp\" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels." [] -is_a: OBI:0000447 ! intra cellular electrophysiology recording assay +is_a: OBI:0000447 ! intracellular electrophysiology recording assay [Term] id: OBI:0002186 @@ -17122,7 +17259,7 @@ is_a: OBI:0002410 ! menopausal status [Term] id: OBI:0002415 name: exposure to environmental and workplace carcinogens history -def: "A information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment." [] +def: "An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment." [] is_a: IAO:0000030 ! information content entity [Term] @@ -18496,51 +18633,57 @@ is_a: OBI:0002677 ! in vivo assay measuring a B cell epitope specific response a [Term] id: OBI:0002639 name: in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden -def: "A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specfic T cells." [] +def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden." [] synonym: "pathogen burden after challenge after adoptive transfer|in vivo assay" EXACT [] -is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells +is_a: OBI:0001475 ! in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden +is_a: OBI:0003470 ! in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0002640 name: in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden -def: "A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on pathogen burden after adoptive transfer of epitope specific antibodies or B cells." [] +def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden." [] synonym: "pathogen burden after challenge after adoptive transfer|in vivo assay" EXACT [] -is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells +is_a: OBI:0002051 ! in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden +is_a: OBI:0003475 ! in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002641 -name: in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival -def: "A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specfic T cells." [] -synonym: "survival from challenge after adoptive transfer|in vivo assay" EXACT [] +name: in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival +def: "An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival." [] +synonym: "survival from other challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001492 ! in vivo assay measuring T cell epitope specific protection based on survival -is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells +is_a: OBI:0003474 ! in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0002642 -name: in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival -def: "A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on survival after adoptive transfer of epitope specific antibodies or B cells." [] -synonym: "survival from challenge after adoptive transfer|in vivo assay" EXACT [] -is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells +name: in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival +def: "An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival." [] +synonym: "survival from other challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001696 ! in vivo assay measuring B cell epitope specific protection based on survival +is_a: OBI:0003479 ! in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002643 -name: in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells -def: "A T cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specfic T cells." [] +name: in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden +def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden." [] synonym: "tumor burden after challenge after adoptive transfer|in vivo assay" EXACT [] -is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells +is_a: OBI:0001473 ! in vivo assay measuring T cell epitope specific protection after tumor burden challenge +is_a: OBI:0003472 ! in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0002644 -name: in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells -def: "A B cell epitope in vivo intervention experiment that uses a epitope protection experiment based on tumor burden after adoptive transfer of epitope specific antibodies or B cells." [] +name: in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden +def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden." [] synonym: "tumor burden after challenge after adoptive transfer|in vivo assay" EXACT [] -is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells +is_a: OBI:0002052 ! in vivo assay measuring B cell epitope specific protection after tumor burden challenge +is_a: OBI:0003477 ! in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002645 name: in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells def: "An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells." [] synonym: "tolerance after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001324 ! in vivo assay measuring T cell epitope specific tolerance induction is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] @@ -18548,6 +18691,7 @@ id: OBI:0002646 name: in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells def: "An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "tolerance after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001693 ! in vivo assay measuring B cell epitope specific tolerance induction is_a: OBI:0002677 ! in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells [Term] @@ -18699,24 +18843,24 @@ is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response a [Term] id: OBI:0002669 -name: biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells +name: assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells def: "A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells." [] -synonym: "antibody help after adoptive transfer|biological activity" EXACT [] -is_a: OBI:0001228 ! biological activity assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response +synonym: "antibody help after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001228 ! in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002670 -name: biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells +name: assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells def: "A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells." [] -synonym: "T cell help after adoptive transfer|biological activity" EXACT [] -is_a: OBI:0001263 ! biological activity assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response +synonym: "T cell help after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001263 ! in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002671 name: in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells -def: "A T cell epitope specific killing assay that uses an in vivo cell mediated cell killing assay after adoptive transfer of epitope specfic T cells." [] +def: "An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells." [] synonym: "cytotoxicity after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001392 ! in vivo assay measuring epitope specific T cell killing is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells @@ -18754,14 +18898,14 @@ id: OBI:0002676 name: in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells def: "An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells." [] synonym: "in vivo response after adoptive transfer|in vivo assay" EXACT [] -is_a: OBI:0001484 ! biological activity assay measuring T cell epitope specific in vivo activity +is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0002677 name: in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells def: "An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "in vivo response after adoptive transfer|in vivo assay" EXACT [] -is_a: OBI:0001698 ! biological activity assay measuring B cell epitope specific in vivo activity +is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0002678 @@ -19988,7 +20132,7 @@ is_a: OBI:0002930 ! light trap [Term] id: OBI:0002933 -name: Mosquito Magnet trap +name: Mosquito Magnet Pro trap def: "An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods." [] is_a: OBI:0002920 ! arthropod trap @@ -21871,7 +22015,7 @@ is_a: IAO:0000027 ! data item [Term] id: OBI:0003244 name: blood microbiology datum -def: "An organism identification assay that is the specified output of a blood microbiology assay." [] +def: "An organism identification datum that is the specified output of a blood microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] @@ -21883,7 +22027,7 @@ is_a: IAO:0000027 ! data item [Term] id: OBI:0003246 name: feces microbiology datum -def: "An organism identification assay that is the specified output of a feces microbiology assay." [] +def: "An organism identification datum that is the specified output of a feces microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] @@ -21895,7 +22039,7 @@ is_a: IAO:0000027 ! data item [Term] id: OBI:0003248 name: urine microbiology datum -def: "An organism identification assay that is the specified output of a urine microbiology assay." [] +def: "An organism identification datum that is the specified output of a urine microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] @@ -21907,7 +22051,7 @@ is_a: IAO:0000027 ! data item [Term] id: OBI:0003251 name: induced sputum microbiology datum -def: "An organism identification assay that is the specified output of an induced sputum microbiology assay." [] +def: "An organism identification datum that is the specified output of an induced sputum microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] @@ -21919,49 +22063,49 @@ is_a: IAO:0000027 ! data item [Term] id: OBI:0003253 name: cerebrospinal fluid microbiology datum -def: "An organism identification assay that is the specified output of a cerebrospinal fluid microbiology assay." [] +def: "An organism identification datum that is the specified output of a cerebrospinal fluid microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] id: OBI:0003254 name: endotracheal aspirate assay datum -def: "An organism identification assay that is the specified output of an endotracheal aspirate assay." [] +def: "An organism identification datum that is the specified output of an endotracheal aspirate assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003255 name: endotracheal tube aspirate microbiology datum -def: "An organism identification assay that is the specified output of an endotracheal tube aspirate microbiology assay." [] +def: "An organism identification datum that is the specified output of an endotracheal tube aspirate microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] id: OBI:0003256 name: lung microbiology datum -def: "An organism identification assay that is the specified output of a lung microbiology assay." [] +def: "An organism identification datum that is the specified output of a lung microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] id: OBI:0003257 name: nasopharyngeal or oropharyngeal swab microbiology datum -def: "An organism identification assay that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay." [] +def: "An organism identification datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] id: OBI:0003258 name: pleural fluid microbiology datum -def: "An organism identification assay that is the specified output of a pleural fluid microbiology assay." [] +def: "An organism identification datum that is the specified output of a pleural fluid microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] id: OBI:0003259 name: umbilical cord blood assay datum -def: "An organism identification assay that is the specified output of an umbilical cord blood assay." [] +def: "An organism identification datum that is the specified output of an umbilical cord blood assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003260 name: umbilical cord blood microbiology datum -def: "An organism identification assay that is the specified output of an umbilical cord blood microbiology assay." [] +def: "An organism identification datum that is the specified output of an umbilical cord blood microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] @@ -22404,8 +22548,8 @@ is_a: OBI:0000070 ! assay [Term] id: OBI:0003369 name: assay kit -def: "A processed material that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit." [] -is_a: OBI:0000047 ! processed material +def: "A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit." [] +is_a: OBI:0000968 ! device [Term] id: OBI:0003371 @@ -22451,7 +22595,7 @@ is_a: OBI:0002649 ! blood microbiology assay [Term] id: OBI:0003382 name: placental blood microbiology datum -def: "An organism identification assay that is the specified output of a placental blood microbiology assay." [] +def: "An organism identification datum that is the specified output of a placental blood microbiology assay." [] is_a: OBI:0003064 ! organism identification datum [Term] @@ -22460,6 +22604,551 @@ name: eukaryota in placental blood datum def: "A placental blood microbiology datum that is interpreted as an indication of the presence of eukaryota in the specimen." [] is_a: OBI:0003382 ! placental blood microbiology datum +[Term] +id: OBI:0003384 +name: synaptosome preparation process +def: "A material component separation process where a synaptic terminal is isolated from a neuron by mild homogenization of nervous tissue under isotonic conditions and subsequent fractionation using differential and density gradient centrifugation." [] +is_a: OBI:0600014 ! material component separation + +[Term] +id: OBI:0003386 +name: Illumina HiSeq 1500 +def: "A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option." [] +synonym: "HiSeq 1500" EXACT [] +is_a: OBI:0400103 ! DNA sequencer + +[Term] +id: OBI:0003387 +name: NextSeq 550 +def: "A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing." [] +is_a: OBI:0400103 ! DNA sequencer + +[Term] +id: OBI:0003388 +name: Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 +def: "A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays." [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003389 +name: Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray +def: "A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays." [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003390 +name: Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray +def: "A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays." [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003391 +name: Affymetrix Mouse Genome 430 2.0 Array +def: "A DNA microarray manufactured by Affymetrix, which includes complete coverage of the GeneChip Mouse Expression Set 430, for analysis of over 39,000 transcripts and variants from more than 34,000 well-characterized mouse genes and UniGene clusters, on a single array. The sequences for this array were selected from GenBank™, dbEST, and RefSeq., and sequence clusters cretaed from the UniGene database." [] +synonym: "GeneChip Mouse Genome 430 2.0 Array" EXACT [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003392 +name: Affymetrix Mouse Genome 430A 2.0 Array +def: "A DNA microarray manufactured by Affymetrix for gene expression analysis focusing on approximately 14,000 well-characterized genes in the transcribed mouse genome using single-array cartridge. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database." [] +synonym: "GeneChip Mouse Genome 430A 2.0 Array" EXACT [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003393 +name: Affymetrix Mouse Gene 1.0 ST Array +def: "A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile." [] +synonym: "GeneChip Mouse Gene 1.0 ST Array" EXACT [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003394 +name: Affymetrix Mouse Gene 2.1 ST Array +def: "A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA).To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db." [] +synonym: "GeneChip Mouse Gene 2.1 ST Array" EXACT [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003395 +name: Affymetrix Rhesus Macaque Genome Array +def: "A DNA microarray manufactured by Affymetrix,which is a single-labeled high-density oligonucleotide array, designed to study gene expression in the rhesus animal model and to interrogate rhesus transcripts orthologous to the 3' end of human transcripts. The array consists of over 52,000 probe sets representing more than 20,000 genes, and several relevant viral organisms for studying host-disease immune response." [] +synonym: "GeneChip Rhesus Macaque Genome Array" EXACT [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003396 +name: Affymetrix Human Transcriptome Array 2.0 +def: "A DNA microarray manufactured by Affymetrix, to go beyond gene-level expression profiling to accurately detect all known transcript isoforms produced by a gene. The array design covers >245,000 coding transcripts, >40,000 non-coding transcripts and >339,000 probe sets covering exon-exon junctions, thus ensuring uniform coverage of the transcriptome." [] +synonym: "GeneChip Human Transcriptome Array 2.0" EXACT [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003397 +name: Affymetrix Human Genome U219 Array +def: "A DNA microarray manufactured by Affymetrix, which comprises more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™." [] +synonym: "Applied Biosystems GeneChip PrimeView Human Gene Expression Array" EXACT [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003398 +name: Affymetrix Human Gene 2.0 ST Array +def: "A DNA microarray manufactured by Affymetrix, which provides the most accurate, sensitive, and comprehensive measurement of protein coding (mRNA) and long intergenic non-coding RNA (lincRNA) transcripts. The array design covers >33,500 coding transcripts and >11,000 lincRNA transcripts thus enabling researchers to understand whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events." [] +synonym: "GeneChip Human Gene 2.0 ST Array" EXACT [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003399 +name: Affymetrix Clariom S Assay, Human +def: "A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the human transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers , and to quickly assess changes in key genes and pathways." [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003400 +name: Affymetrix Clariom S Assay, Mouse +def: "A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the mouse transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers, and to quickly assess changes in key genes and pathways." [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003401 +name: Illumina HumanHT-12 V4.0 expression beadchip +def: "An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling and expression-based quantitative trait loci (eQTL) studies. This BeadChip contains 12 arrays, each featuring more than 48,000 probes, targeting more than 31,000 annotated genes, providing genome-wide coverage of well-characterized genes, gene candidates, and splice variants." [] +is_a: OBI:0001869 ! Illumina BeadChip + +[Term] +id: OBI:0003402 +name: Illumina MouseRef-8 v2.0 beadchip +def: "An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling in the mouse.This Beadchip contains 8 microarrays, featuring more than 25,000 probes per array, derived from the NCBI RefSeq database and supplemented with MEEBO and RIKEN FANTOM2 content." [] +is_a: OBI:0001869 ! Illumina BeadChip + +[Term] +id: OBI:0003403 +name: Affymetrix Mouse Exon Junction Array +def: "A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the mouse transcriptome." [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003404 +name: Affymetrix Human Exon Junction Array +def: "A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the human transcriptome." [] +is_a: OBI:0400148 ! DNA microarray + +[Term] +id: OBI:0003413 +name: administering substance in vivo to cause disease +def: "An administration of substance in vivo with the intention to induce disease in the organism." [] +is_a: OBI:0600007 ! administering substance in vivo + +[Term] +id: OBI:0003414 +name: administering substance in vivo to reduce or prevent disease +def: "An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism." [] +is_a: OBI:0600007 ! administering substance in vivo + +[Term] +id: OBI:0003415 +name: peripheral blood mononuclear cell specimen +def: "A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system." [] +synonym: "PBMC specimen" EXACT [] +is_a: OBI:0100051 ! specimen + +[Term] +id: OBI:0003416 +name: mid-upper arm circumference datum +def: "A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm." [] +is_a: IAO:0000408 ! length measurement datum + +[Term] +id: OBI:0003417 +name: antigen specific antibodies assay datum +def: "A data item that is the specified output of an antigen specific antibodies assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003418 +name: antigen specific antibodies in blood assay +def: "An antigen specific antibodies assay that has a blood specimen as evaluant." [] +is_a: OBI:0002145 ! antigen specific antibodies assay +is_a: OBI:0003040 ! blood assay + +[Term] +id: OBI:0003419 +name: antigen specific antibodies in milk assay +def: "An antigen specific antibodies assay that has a milk specimen as evaluant." [] +is_a: OBI:0002145 ! antigen specific antibodies assay + +[Term] +id: OBI:0003420 +name: antigen specific antibodies in blood assay datum +def: "An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay." [] +is_a: OBI:0003243 ! blood assay datum + +[Term] +id: OBI:0003421 +name: antigen specific antibodies in milk assay datum +def: "An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay." [] +is_a: OBI:0003365 ! milk assay datum + +[Term] +id: OBI:0003422 +name: enzymatic activity level assay +def: "An assay in which the level of catalytic activity of an enzyme is determined." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003423 +name: 5'-nucleotidase activity level assay +def: "An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003424 +name: alanine aminotransferase activity level assay +def: "An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003425 +name: alkaline phosphatase activity level assay +def: "An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003426 +name: amylase activity level assay +def: "An enzymatic activity level assay that measures the activity of amylase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003427 +name: aspartate aminotransferase activity level assay +def: "An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003428 +name: cholinesterase activity level assay +def: "An enzymatic activity level assay that measures the activity of cholinesterase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003429 +name: creatine kinase activity level assay +def: "An enzymatic activity level assay that measures the activity of creatine kinase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003430 +name: gamma-glutamyltransferase activity level assay +def: "An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003431 +name: glutamate dehydrogenase activity level assay +def: "An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003432 +name: isocitrate dehydrogenase activity level assay +def: "An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003433 +name: lactate dehydrogenase activity level assay +def: "An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003434 +name: sorbitol dehydrogenase activity level assay +def: "An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003435 +name: acyl-CoA oxidase activity level assay +def: "An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003436 +name: N-acetyl-beta-glucosaminidase activity level assay +def: "An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003437 +name: ribonuclease activity level assay +def: "An enzymatic activity level assay that measures the activity of ribonuclease in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003438 +name: galactosidase activity level assay +def: "An enzymatic activity level assay that measures the activity of galactosidase in a sample." [] +is_a: OBI:0003422 ! enzymatic activity level assay + +[Term] +id: OBI:0003454 +name: Mosquito Magnet Liberty Plus trap +def: "An arthropod trap that is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor." [] +is_a: OBI:0002920 ! arthropod trap + +[Term] +id: OBI:0003455 +name: tumor challenge +def: "The administration of a malignant cell to a host." [] +is_a: OBI:0003456 ! in vivo challenge + +[Term] +id: OBI:0003456 +name: in vivo challenge +def: "The administration of a challenge to a live host." [] +is_a: OBI:0600007 ! administering substance in vivo + +[Term] +id: OBI:0003457 +name: epitope protection from infectious challenge experiment based on survival +def: "An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls." [] +synonym: "survival after infectious challenge" EXACT [] +is_a: OBI:0001179 ! epitope protection from infectious challenge experiment + +[Term] +id: OBI:0003458 +name: epitope protection from tumor challenge experiment based on burden +def: "An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls." [] +synonym: "burden after tumor challenge " EXACT [] +is_a: OBI:0001183 ! epitope protection from tumor challenge experiment + +[Term] +id: OBI:0003459 +name: epitope protection from tumor challenge experiment based on survival +def: "An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls." [] +synonym: "survival after tumor challenge" EXACT [] +is_a: OBI:0001183 ! epitope protection from tumor challenge experiment + +[Term] +id: OBI:0003460 +name: in vivo assay measuring T cell epitope specific protection from pathogen challenge +def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge." [] +synonym: "protection from pathogen challenge|in vivo assay" EXACT [] +is_a: OBI:0001179 ! epitope protection from infectious challenge experiment +is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge + +[Term] +id: OBI:0003461 +name: in vivo assay measuring T cell epitope specific protection from tumor challenge +def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge." [] +synonym: "protection from tumor challenge|in vivo assay" EXACT [] +is_a: OBI:0001183 ! epitope protection from tumor challenge experiment +is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge + +[Term] +id: OBI:0003462 +name: in vivo assay measuring T cell epitope specific protection from other challenge +def: "An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor." [] +synonym: "protection from other challenge|in vivo assay" EXACT [] +is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge + +[Term] +id: OBI:0003463 +name: in vivo assay measuring T cell epitope specific survival after tumor challenge +def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival." [] +synonym: "survival from tumor challenge|in vivo assay" EXACT [] +is_a: OBI:0003459 ! epitope protection from tumor challenge experiment based on survival +is_a: OBI:0003461 ! in vivo assay measuring T cell epitope specific protection from tumor challenge + +[Term] +id: OBI:0003464 +name: in vivo assay measuring T cell epitope specific survival after pathogen challenge +def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival." [] +synonym: "survival from pathogen challenge|in vivo assay" EXACT [] +is_a: OBI:0003457 ! epitope protection from infectious challenge experiment based on survival +is_a: OBI:0003460 ! in vivo assay measuring T cell epitope specific protection from pathogen challenge + +[Term] +id: OBI:0003465 +name: in vivo assay measuring B cell epitope specific protection from pathogen challenge +def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge." [] +synonym: "protection from pathogen challenge|in vivo assay" EXACT [] +is_a: OBI:0001179 ! epitope protection from infectious challenge experiment +is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge + +[Term] +id: OBI:0003466 +name: in vivo assay measuring B cell epitope specific protection from tumor challenge +def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge." [] +synonym: "protection from tumor challenge|in vivo assay" EXACT [] +is_a: OBI:0001183 ! epitope protection from tumor challenge experiment +is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge + +[Term] +id: OBI:0003467 +name: in vivo assay measuring B cell epitope specific protection from other challenge +def: "An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor." [] +synonym: "protection from other challenge|in vivo assay" EXACT [] +is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge + +[Term] +id: OBI:0003468 +name: in vivo assay measuring B cell epitope specific survival after pathogen challenge +def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival." [] +synonym: "survival from pathogen challenge|in vivo assay" EXACT [] +is_a: OBI:0003457 ! epitope protection from infectious challenge experiment based on survival +is_a: OBI:0003465 ! in vivo assay measuring B cell epitope specific protection from pathogen challenge + +[Term] +id: OBI:0003469 +name: in vivo assay measuring B cell epitope specific survival after tumor challenge +def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival." [] +synonym: "survival from tumor challenge|in vivo assay" EXACT [] +is_a: OBI:0003459 ! epitope protection from tumor challenge experiment based on survival +is_a: OBI:0003466 ! in vivo assay measuring B cell epitope specific protection from tumor challenge + +[Term] +id: OBI:0003470 +name: in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells +def: "An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells." [] +synonym: "protection from pathogen challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001179 ! epitope protection from infectious challenge experiment +is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells + +[Term] +id: OBI:0003471 +name: in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival +def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival." [] +synonym: "survival after pathogen challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0003464 ! in vivo assay measuring T cell epitope specific survival after pathogen challenge +is_a: OBI:0003470 ! in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells + +[Term] +id: OBI:0003472 +name: in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells +def: "An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells." [] +synonym: "protection from tumor challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001183 ! epitope protection from tumor challenge experiment +is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells + +[Term] +id: OBI:0003473 +name: in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival +def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival." [] +synonym: "survival after tumor challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0003463 ! in vivo assay measuring T cell epitope specific survival after tumor challenge +is_a: OBI:0003472 ! in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells + +[Term] +id: OBI:0003474 +name: in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells +def: "An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells." [] +synonym: "protection from other challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells + +[Term] +id: OBI:0003475 +name: in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells +def: "An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells." [] +synonym: "protection from pathogen challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001179 ! epitope protection from infectious challenge experiment +is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells + +[Term] +id: OBI:0003476 +name: in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival +def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival." [] +synonym: "survival after pathogen challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0003468 ! in vivo assay measuring B cell epitope specific survival after pathogen challenge +is_a: OBI:0003475 ! in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + +[Term] +id: OBI:0003477 +name: in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells +def: "An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells." [] +synonym: "protection from tumor challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0001183 ! epitope protection from tumor challenge experiment +is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells + +[Term] +id: OBI:0003478 +name: in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival +def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival." [] +synonym: "survival after tumor challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0003469 ! in vivo assay measuring B cell epitope specific survival after tumor challenge +is_a: OBI:0003477 ! in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells + +[Term] +id: OBI:0003479 +name: in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells +def: "An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells." [] +synonym: "protection from other challenge after adoptive transfer|in vivo assay" EXACT [] +is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells + +[Term] +id: OBI:0003480 +name: Gram stain assay +def: "An organism identification assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003481 +name: cow-baited arthropod trap +def: "A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent." [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0003482 +name: lymph specimen +def: "A specimen that is derived from a portion of lymph collected from an organism." [] +is_a: OBI:2000009 ! bodily fluid specimen + +[Term] +id: OBI:0003483 +name: digestive tract specimen +def: "A specimen that is derived from part of a digestive tract." [] +is_a: OBI:0100051 ! specimen + +[Term] +id: OBI:0003484 +name: assay measuring epitope specific interleukin-25 production by T cells +def: "A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells." [] +synonym: "IL-25 release|biological activity" EXACT [] +is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells + +[Term] +id: OBI:0003485 +name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells +def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells." [] +synonym: "IL-25 release|RNA/DNA detection" EXACT [] +is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes +is_a: OBI:0003484 ! assay measuring epitope specific interleukin-25 production by T cells + +[Term] +id: OBI:0003486 +name: intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells +def: "A flow cytometry assay that detects interleukin-25 production by T cells." [] +synonym: "IL-25 release|ICS" EXACT [] +is_a: OBI:0000916 ! flow cytometry assay +is_a: OBI:0003484 ! assay measuring epitope specific interleukin-25 production by T cells + +[Term] +id: OBI:0003487 +name: ELISA measuring epitope specific interleukin-25 production by T cells +def: "An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells." [] +synonym: "IL-25 release|ELISA" EXACT [] +is_a: OBI:0000661 ! enzyme-linked immunosorbent assay +is_a: OBI:0003484 ! assay measuring epitope specific interleukin-25 production by T cells + +[Term] +id: OBI:0003488 +name: cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells +def: "A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells." [] +synonym: "TNF release|bioassay" EXACT [] +is_a: OBI:0000904 ! reporter cell line analyte detection bioassay +is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells + [Term] id: OBI:0005246 name: injection function @@ -22639,6 +23328,7 @@ disjoint_from: OBI:0600013 ! information acquisition [Term] id: OBI:0200001 name: geometric mean calculation +def: "A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations)." [] comment: A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation @@ -23921,7 +24611,7 @@ is_a: IAO:0000030 ! information content entity [Term] id: OBI:0302840 name: curated information -def: "A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts." [] +def: "An information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts." [] is_a: IAO:0000030 ! information content entity [Term] @@ -26074,14 +26764,15 @@ is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell ep [Term] id: OBI:1110130 -name: biological activity assay measuring epitope specific T cell killing +name: assay measuring epitope specific T cell killing def: "A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|biological activity" EXACT [] +is_a: OBI:0000882 ! cell-cell killing assay is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:1110131 -name: biological activity assay measuring epitope specific proliferation of T cells +name: assay measuring epitope specific proliferation of T cells def: "A T cell epitope dependent biological activity assay that detects T cell proliferation." [] synonym: "proliferation|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding @@ -26096,9 +26787,10 @@ is_a: PR:000000001 ! protein [Term] id: OBI:1110150 name: 51 chromium assay measuring epitope specific T cell killing -def: "A T cell epitope specific killing assay performed in vitro that uses a chromium release assay." [] +def: "A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|51 chromium" EXACT [] is_a: OBI:0002062 ! in vitro assay measuring epitope specific T cell killing +is_a: OBI:9999994 ! chromium release assay [Term] id: OBI:1110151 @@ -26134,11 +26826,11 @@ is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by [Term] id: OBI:1110155 -name: ELISA measuring epitope specific tumor necrosis factor production by T cells -def: "An enzyme-linked immunosorbent assay that detects tumor necrosis factor production by T cells." [] +name: ELISA measuring epitope specific tumor necrosis factor alpha production by T cells +def: "An enzyme-linked immunosorbent assay that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|ELISA" EXACT [] is_a: OBI:0001246 ! ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells [Term] id: OBI:1110156 @@ -26214,11 +26906,11 @@ is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110168 -name: ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells -def: "An enzyme-linked immunospot assay that detects tumor necrosis factor production by T cells." [] +name: ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells +def: "An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells" [] synonym: "TNFa release|ELISPOT" EXACT [] is_a: OBI:0001272 ! ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells [Term] id: OBI:1110170 @@ -26254,11 +26946,11 @@ is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by [Term] id: OBI:1110174 -name: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor production by T cells -def: "A flow cytometry assay that detects tumor necrosis factor production by T cells." [] +name: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells +def: "A flow cytometry assay that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|ICS" EXACT [] is_a: OBI:0001385 ! intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells -is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor production by T cells +is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells [Term] id: OBI:1110175 @@ -26296,15 +26988,17 @@ is_a: OBI:1110124 ! assay measuring qualitative binding of a T cell epitope:MHC: [Term] id: OBI:1110180 name: 3H-thymidine assay measuring epitope specific proliferation of T cells -def: "A T cell epitope specific proliferation assay performed on cells in vitro that uses a tritiated thymidine incorporation assay." [] +def: "A tritiated thymidine incorporation assay that detects T cell epitope specific proliferation in vitro." [] synonym: "proliferation|3H-thymidine" EXACT [] +is_a: OBI:0000669 ! tritiated thymidine incorporation assay is_a: OBI:0002071 ! in vitro assay measuring epitope specific proliferation of T cells [Term] id: OBI:1110181 name: BrdU assay measuring epitope specific proliferation of T cells -def: "A T cell epitope specific proliferation assay performed on cells in vitro that uses a BrdU incorporation assay." [] +def: "A BrdU incorporation assay that detects T cell epitope specific proliferation in vitro." [] synonym: "proliferation|BrdU" EXACT [] +is_a: OBI:0000664 ! BrdU incorporation assay is_a: OBI:0002071 ! in vitro assay measuring epitope specific proliferation of T cells [Term] @@ -29765,10 +30459,16 @@ name: contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [] is_a: SO:0000353 ! sequence_assembly +[Term] +id: SO:0000235 +name: TF_binding_site +def: "A DNA site where a transcription factor binds." [] +is_a: SO:0005836 ! regulatory_region + [Term] id: SO:0000276 name: miRNA -def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [] +def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [] is_a: SO:0000001 ! region [Term] @@ -29795,6 +30495,12 @@ name: experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [] is_a: SO:0000001 ! region +[Term] +id: SO:0005836 +name: regulatory_region +def: "A region of sequence that is involved in the control of a biological process." [] +is_a: SO:0000001 ! region + [Term] id: UBERON:0000002 name: uterine cervix @@ -30044,7 +30750,7 @@ is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001264 name: pancreas -def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]." [] +def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] @@ -30065,6 +30771,18 @@ name: cerebrospinal fluid def: "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord." [] is_a: UBERON:0006314 ! bodily fluid +[Term] +id: UBERON:0001460 +name: arm +def: "The part of the forelimb extending from the shoulder to the autopod[cjm]." [] +is_a: UBERON:0000465 ! material anatomical entity + +[Term] +id: UBERON:0001555 +name: digestive tract +def: "A tube extending from the mouth to the anus." [] +is_a: UBERON:0000465 ! material anatomical entity + [Term] id: UBERON:0001557 name: upper respiratory tract @@ -30269,6 +30987,12 @@ name: bone marrow def: "The soft tissue that fills the cavities of bones." [] is_a: UBERON:0000479 ! tissue +[Term] +id: UBERON:0002391 +name: lymph +def: "Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]." [] +is_a: UBERON:0006314 ! bodily fluid + [Term] id: UBERON:0002409 name: pericardial fluid @@ -30960,6 +31684,8 @@ is_a: BFO:0000051 ! has part [Typedef] id: OBI:0001950 name: has performer +def: "A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process." [] +comment: The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant @@ -31176,6 +31902,14 @@ name: has component def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] is_a: BFO:0000051 ! has part +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process." [] +synonym: "has function realized in" EXACT [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process + [Typedef] id: RO:0002219 name: surrounded by diff --git a/views/obi_core.owl b/views/obi_core.owl index e64cfed4..735da5b0 100644 --- a/views/obi_core.owl +++ b/views/obi_core.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -78,7 +78,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2022-07-11 + 2022-12-14 @@ -1595,6 +1595,7 @@ every c that is a concretization of g specifically denotes r BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) @@ -1715,12 +1716,10 @@ every c that is a concretization of g specifically denotes r cell - cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell - cell @@ -2471,10 +2470,23 @@ Request that IAO either clarify these or change definitions not to use them + + + + Metazoa + metazoans + multicellular animals + + Metazoa + + + + - + Bilateria Bilateria @@ -2514,7 +2526,6 @@ Request that IAO either clarify these or change definitions not to use themHomo sapiens human human being - man Homo sapiens