diff --git a/obi.owl b/obi.owl index 53ffa631..e19c5346 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. - 2020-12-16 + 2021-04-06 @@ -128,13 +128,21 @@ + 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 @@ -182,7 +190,9 @@ 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 @@ -209,6 +219,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -991,6 +1002,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + label label @@ -4589,6 +4601,42 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + + + + + + 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 + + + + @@ -4601,6 +4649,54 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + + + + + + 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 + + + + @@ -4624,6 +4720,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + homocysteine + A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. + + homocysteine + + + + @@ -4636,6 +4744,42 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -4648,6 +4792,42 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -4696,6 +4876,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + iron cation + + iron cation + + + + @@ -4708,6 +4899,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + amikacin + An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. + + amikacin + + + + @@ -4720,6 +4923,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + uric acid + An oxopurine that is the final oxidation product of purine metabolism. + + uric acid + + + + @@ -4731,6 +4946,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -4743,6 +4982,65 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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+) + + + + @@ -4767,6 +5065,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + thyroxine + An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. + + thyroxine + + + + @@ -4856,6 +5166,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + elemental oxygen + + elemental oxygen + + + + @@ -4950,6 +5271,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hemoglobin + + hemoglobin + + + + @@ -4961,6 +5293,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + phosphate ion + A phosphorus oxoanion that is the conjugate base of phosphoric acid. + + phosphate ion + + + + @@ -4973,6 +5317,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + folic acids + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + + folic acids + + + + @@ -5056,6 +5412,41 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + calcium cation + + calcium cation + + + + + + + + + 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 + + + + @@ -5085,6 +5476,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -5108,6 +5511,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -5280,6 +5707,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + tacrolimus hydrate + A hydrate that is the monohydrate form of tacrolimus. + + tacrolimus hydrate + + + + @@ -5292,6 +5731,29 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + thyroid stimulating hormone + + thyroid 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 + + + + @@ -5402,11 +5864,18 @@ 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 @@ -5427,9 +5896,14 @@ 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 @@ -5439,9 +5913,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ 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 @@ -5463,9 +5943,16 @@ 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 @@ -5649,6 +6136,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + mesothelial cell + A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + + mesothelial cell + + + + @@ -5697,6 +6197,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -5715,6 +6227,7 @@ 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 @@ -5759,6 +6272,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -5771,6 +6296,45 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -5838,6 +6402,32 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + 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 + + + + @@ -5886,6 +6476,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -5898,6 +6500,42 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + + + + + + 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 + + + + @@ -6088,10 +6726,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - platelet activating factor production - The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels. - platelet activating factor production @@ -6156,6 +6791,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -6252,6 +6899,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -6594,7 +7253,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ 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. + 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 @@ -7038,7 +7697,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ 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. + 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 @@ -7434,10 +8093,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - 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 + 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 + oncostatin M production @@ -7502,6 +8161,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -7646,6 +8317,54 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + 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 + + + + @@ -16405,7 +17124,7 @@ Proposal is to obsolete. - + @@ -19473,7 +20192,9 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 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 @@ -34552,15 +35273,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -34817,15 +35533,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -35007,15 +35718,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -35043,15 +35749,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -35290,39 +35991,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -35385,15 +36057,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -35447,15 +36114,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -35483,15 +36145,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -35597,15 +36254,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -35994,15 +36646,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -36066,15 +36713,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -36334,39 +36976,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -36394,15 +37007,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -36538,15 +37146,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -36744,15 +37347,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -36852,15 +37450,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -37119,15 +37712,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -37207,15 +37795,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -37594,15 +38177,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -37846,6 +38424,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 + @@ -38012,25 +38591,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - + + + + @@ -38110,15 +38674,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -38284,15 +38843,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -38622,15 +39176,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -38684,25 +39233,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - + + + + @@ -39105,15 +39639,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -39505,15 +40034,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -39713,15 +40237,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -39775,15 +40294,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -39811,15 +40325,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -40130,15 +40639,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -40333,15 +40837,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - - + + + + @@ -40542,15 +41041,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - - + + + + @@ -40605,15 +41099,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - - + + + + @@ -41063,15 +41552,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - - + + + + @@ -41251,15 +41735,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -41374,15 +41853,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -41410,15 +41884,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -41446,15 +41915,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -41581,15 +42045,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -41643,15 +42102,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -41851,15 +42305,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -42631,44 +43080,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -42722,15 +43137,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -45282,15 +45692,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + @@ -45695,15 +46100,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + @@ -46166,15 +46566,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + @@ -46386,15 +46781,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + @@ -47335,25 +47725,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -47379,25 +47754,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -47422,25 +47782,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -47468,25 +47813,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -47514,25 +47844,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -47560,25 +47875,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -49260,25 +49560,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -49310,25 +49595,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -49356,25 +49626,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -49684,15 +49939,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - + + + + @@ -49718,20 +49968,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - + + + - - - - - - - + + - - + + @@ -49787,20 +50032,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - + + + - - - - - - - + + - - + + @@ -51649,15 +51889,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -51685,15 +51920,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -51721,15 +51951,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -51757,15 +51982,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -51793,15 +52013,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -51829,15 +52044,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -51865,15 +52075,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -51901,15 +52106,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -52694,15 +52894,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -52730,15 +52925,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -61123,20 +61313,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - + + + - - - - - - - + + - - + + @@ -61164,15 +61349,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - + + + + @@ -61200,15 +61380,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - + + + + @@ -61236,15 +61411,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - + + + + @@ -61651,15 +61821,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - + + + + @@ -62998,15 +63163,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -67121,15 +67281,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -69814,14 +69969,7 @@ https://www.doi.org/ - - - - - - - - + @@ -72181,25 +72329,10 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + @@ -72223,25 +72356,10 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + @@ -72270,15 +72388,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -72306,41 +72419,10 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -72364,41 +72446,10 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -72427,15 +72478,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -75567,7 +75613,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -75762,6 +75808,565 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + specimen collection device + + A container used to collect a specimen. + https://orcid.org/0000-0002-8844-9165 + specimen collection device + + + + + + + + + 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 + + + + + + + + + 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 + sponge stick + polyprobe + sponge probe + sponge-stick + https://medical-dictionary.thefreedictionary.com/swab + specimen collection swab stick + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + @@ -75850,10 +76455,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + Person: Chris Stoeckert + Person: Jie Zheng + Person: Chris Stoeckert + Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB solar light source @@ -76217,8 +76822,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 BG-Sentinel trap catch - VSMO:0001906 - IRO:0000028 + IRO:0000028 + VSMO:0001906 https://github.com/obi-ontology/obi/issues/1217 BG-Sentinel trap @@ -76266,8 +76871,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 catch - VSMO:0001295 - IRO:0000029 + IRO:0000029 + VSMO:0001295 https://github.com/obi-ontology/obi/issues/1217 encephalitis virus surveillance trap @@ -76394,8 +76999,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 - Parasites Vectors 8, 239 (2015) - IRO:0000154 + IRO:0000154 + Parasites Vectors 8, 239 (2015) https://github.com/obi-ontology/obi/issues/1217 Onderstepoort Veterinary Institute light-suction trap @@ -76427,8 +77032,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 - VSMO:0001501 - MIRO:30000016 + MIRO:30000016 + VSMO:0001501 https://github.com/obi-ontology/obi/issues/1217 ovitrap @@ -76602,1842 +77207,2184 @@ 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 + + + 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. + + 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 - + - - + + + 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. + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + - + - + - - + + - - + + - - - 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. + + magnetic resonance imaging assay - 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 + 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 - + - - - chimera + + + + + + + + + + + + + + + + + + + + + + + + + + + computed tomography imaging assay - 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 + 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 - + - - + + - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - 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. + positron emission tomography imaging assay - 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 + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - + - + - - - - - - + + + + + + + + + + + + - 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 + 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 - + - - - obsolete_immortal cell - a single Hela cell + + + T cell receptor repertoire sequencing assay - 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 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 - + - - - 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 + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + 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 + + + + + + + + + - + - + - - - 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 + + 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 - + - - - obsolete_cell line cell + + + 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 material entity that represents generations of a primary culture. - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch - - obsolete_cell line cell - true + 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 - + - - - obsolete_immortal cell line culture + + + arthropod attractor role - 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 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 - + - - - - - - - - - - - - - - - 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 + + + arthropod collection process with automated identification - 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 + 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 - - - - - - - - - - - - - - - - - - - - - - - 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). + + + gravid female arthropod specimen collection process - 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 + 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 - + - - - - - - - - - - - - - - - - - - 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) + + + resting flight-capable arthropod specimen collection process - 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 + 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 - - - - - - - 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'." + + + daytime arthropod specimen collection by aspiration - 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 + 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 - + - - - cultured clonal cell population - cell cut -Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 + + + 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 + + + + + + + + + landing arthropod specimen collection process - 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 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 - + - - - 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] + + + flying adult arthropod collection process by passive interception - 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 + 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 - + - - - - - - - - - - - - - - - synthetic peptide - the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme + + + device for resting of adult arthropods for collection - 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 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 resting of adult arthropods for collection - + - - - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - bronchial alveolar lavage - solution containing lung derived T cells, eosinophils, and TNFa. + + + arthropod trap containing small non-human animal bait - 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 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 - + - - - obsolete_polymer + + + trap for emerging adult arthropods - 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 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 - + - - - - - - - - - glucose in solution - Glucose present in blood - - A scattered aggregate of glucose molecules in a liquid - PERSON: Jie Zheng - glucose molecules - glucose in solution + + + + + + + + + + + + + + + + + + + ferritin assay + + An assay that measures ferritin + James A. Overton, ORCID:0000-0001-5139-5557 + OBI + ferritin assay - + - + - - - - - - - - - - + + + - + - - - - - - - - - + + + + - - - - - - - - - - - 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 + + + + + fibrinogen assay + + An assay that measures fibrinogen + James A. Overton, ORCID:0000-0001-5139-5558 + OBI + fibrinogen assay - + - - - - - + + - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - geometric mean calculation - - 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). - geometric mean calculation + + + iron assay + + An analyte assay that measures the abundance of iron + James A. Overton, ORCID:0000-0001-5139-5559 + OBI + iron assay - + - - - - - - - - - logistic-log curve fitting - Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve. - - A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). - Elisabetta Manduchi - James Malone - Melanie Courtot - Ryan Brinkman - ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 - logistic-log curve fitting + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - - - - - - - logit-log curve fitting - Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively. - - A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. - The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model. - Elisabetta Manduchi - James Malone - Melanie Courtot - Ryan Brinkman - ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 - logit-log curve fitting + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transferrin assay + + An analyte assay that measures the abundance of transferrin + James A. Overton, ORCID:0000-0001-5139-5562 + OBI + transferrin assay - + - - - - - - - - - log-log curve fitting - Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. - - A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. - Elisabetta Manduchi - James Malone - Melanie Courtot - Ryan Brinkman - ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 - log-log curve fitting + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - 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 - James Malone - TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction - feature extraction objective + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + globulin assay + + An analyte assay that measures the abundance of globulin + James A. Overton, ORCID:0000-0001-5139-5564 + OBI + globulin assay - + - - - - - + + + - + + + + + + + + + + + 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 + + + + + + + + + + + - - + + + + + + + - - - - - - - - biexponential transformation - This type of transformation is typically used in flow cytometry. - - A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - biexponential transformation + + + 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 - + - - - - - - - - - box-cox transformation - - A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. - Ryan Brinkman - ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. - box-cox transformation + + + + + + + + + + + + + + + + + + + hematocrit assay + + A cytometry assay that measures the proportion of red blood cells + James A. Overton, ORCID:0000-0001-5139-5567 + OBI + hematocrit assay - + - - - - - - - - - hyperlog transformation - This type of transformation is typically used in flow cytometry - - A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42." - http://flowcyt.sourceforge.net/gating/latest.pdf - hyperlog transformation + + + + + + + + + + + + + + + + + + + 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 - + - - - loess scale group transformation one-channel - Loess scale group normalization applied to data from two one-channel expression microarray assays. - - A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. - Elisabetta Manduchi - OTHER: Editor's adjustment based on MGED Ontology term - loess scale group transformation one-channel + + + + + + + + + + + + + + + + + + + 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 - + - - - - - - - - - logical transformation - This type of transformation is typically used in flow cytometry. - - A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - logical transformation + + + + + + + + + + + + + + + + + + + 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 - + - - - loess scale group transformation two-channel - Loess scale group normalization applied to data from a two-channel expression microarray assay. - - A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. - Elisabetta Manduchi - OTHER: Adjusted from MGED Ontology - loess scale group transformation two-channel + + + + + + + + + + + + + + + + + + + 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 - + - - - loess global transformation one-channel - Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. - - A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. - Elisabetta Manduchi - OTHER: Editor's generalization based on MGED Ontology term - loess global transformation one-channel + + + + + + + + + + + + + + + + + + + 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 - + - - - split-scale transformation - This type of transformation is typically used in flow cytometry - - A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - split-scale transformation + + + + + + + + + + + + + + + + + + + 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 - + - - - loess global transformation two-channel - Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. - - A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. - Elisabetta Manduchi - OTHER: Editor's generalization based on MGED Ontology term - loess global transformation two-channel + + + + + + + + + + + + + + + + + + + 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 - + - - - - - - - - - sine transformation - sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc. - - A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. - Elisabetta Manduchi - WEB: http://mathworld.wolfram.com/Sine.html - sine transformation + + + + + + + + + + + + + + + + + + + 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 - + - - - - - - - - - cosine transformation - cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc. - - 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 - WEB: http://mathworld.wolfram.com/Cosine.html - cosine transformation + + + + + + + + + + + + + + + + + + + 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 - + - - - loess group transformation one-channel - A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. + + + injection function - A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. - Elisabetta Manduchi - OTHER: Editor's generalization based on MGED Ontology term - loess group transformation one-channel + 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 - + - - - loess group transformation two-channel - A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. - - A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. - Elisabetta Manduchi - OTHER: Editor's generalization based on MGED Ontology term - loess group transformation two-channel + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - homogeneous polynomial transformation - a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables. - - A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. - Elisabetta Manduchi - WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html - homogeneous polynomial transformation + + + chimera + + An organism which contains cells or tissues with a different genotype + PERSON: Helen Parkinson + GROUP: OBI + chimera - + - - - - - - - - - linlog transformation - This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. - - 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 - PMID: 16646782 - linlog transformation + + + 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 - + - - + + + + + + + + + + + + + - - + + + + + + + + + + + + - variance stabilizing transformation - This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536. - - A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper. - Elisabetta Manduchi - James Malone - Melanie Courtot - variance stabilising transformation - PMID: 12169536 - variance stabilizing transformation - - - - - - - - - loess global transformation - - A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - OTHER: Editor's generalization based on MGED Ontology term - loess global transformation - - - - - - - - - loess group transformation - - A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - OTHER: Editor's generalization based on MGED Ontology term - loess group transformation + 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 - + - - + + - - + + + + + + + + + + + + + + + + + + - - + + - loess scale group transformation - - A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. - Elisabetta Manduchi - James Malone - Melanie Courtot - OTHER: Editor's generalization based on MGED Ontology term - loess scale group transformation + 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 - + - - - - - - - - - total intensity transformation single - This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). + + + + + + + + + + + + + organism + animal + fungus + plant + virus - A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. - Elisabetta Manduchi - Helen Parkinson - James Malone - Melanie Courtot - 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 + 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 - + - - - - - - - - - total intensity transformation paired - This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. - - 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 - 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 + + + 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 + + + + + + + + - - - - - - - - - - - - + + + + + + + + + + + + + + - - + + + + + + + + + + + + - quantile transformation - This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. - - A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - quantile transformation - - - - - - - - - - + + - mean centering - This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered. + 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. - 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 - mean centring - PERSON: Elisabetta Manduchi - mean centering + 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 - + - - - - - - - - - median centering - This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered. + + + + + + + + + + + + + + specimen + Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. - 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 - median centring - PERSON: Elisabetta Manduchi - median centering + 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 - + - - - differential expression analysis objective - Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software - - A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - differential expression analysis objective + + + 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 - + - - - - - - - - - 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 method + + + 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 - + - - + + - - + + - 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 - - 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 - - - - - - - - - - + + - jackknifing method - simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure + 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 - 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 - jackknifing method + 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 - + - - + + - - + + - 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. + + + + + + + + + + + + + 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). - 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 - boostrapping + 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 + - 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) + 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 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 - Philippe Rocca-Serra - Helen Parkinson - Benjamini and Hochberg false discovery rate correction method + 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. + - + - - - - - - - - - pareto scaling - - A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. - Elisabetta Manduchi - Philippe Rocca-Serra - PMID:16762068 - pareto scaling + + + 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 - + - - - modular decomposition + + + cultured clonal cell population + cell cut +Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 - Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. - Tina Hernandez-Boussard - editor - modular decomposition + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - 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 - James Malone - Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/K-means - k-means clustering + + + 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 - + - - - - + + + - - - - - - + + - - hierarchical clustering - - A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). - James Malone - WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering - hierarchical clustering + + + + 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 - + - - - average linkage hierarchical clustering + + + + + + + + + + + + + + + + + + + + + + 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 - An average 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 average distance between objects from the first cluster and objects from the second cluster. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - average linkage hierarchical clustering + 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 - + - - - complete linkage hierarchical clustering + + + + + + + + + + + + + + + bronchial alveolar lavage + solution containing lung derived T cells, eosinophils, and TNFa. - an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - complete linkage hierarchical clustering + 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 - + - - - 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 - PERSON: Elisabetta Manduchi - single linkage hierarchical clustering + + + 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 + + + + + + + + - - + + - + + - - + + + + + + + + + + + + + + + + + - - + + - 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) - - 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 - Philippe Rocca-Serra - Helen Parkinson - Benjamini and Yekutieli false discovery rate correction method + + 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 - + - + - + + - + - + - dimensionality reduction - - A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - data projection - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - dimensionality reduction + + + + + + + geometric mean calculation + + 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). + geometric mean calculation - + - - - principal components analysis dimensionality reduction + + + + + + + + + logistic-log curve fitting + Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve. - A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. + A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). Elisabetta Manduchi James Malone Melanie Courtot - Philippe Rocca-Serra - pca data reduction - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - principal components analysis dimensionality reduction + Ryan Brinkman + ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 + logistic-log curve fitting - + - - - probabilistic algorithm - - A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. + + + + + + + + + logit-log curve fitting + Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively. + + A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. + The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model. + Elisabetta Manduchi James Malone - PERSON: James Malone - probabilistic algorithm + Melanie Courtot + Ryan Brinkman + ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 + logit-log curve fitting - + - - - expectation maximization - - EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. + + + + + + + + + log-log curve fitting + Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. + + A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. + Elisabetta Manduchi James Malone - PERSON: James Malone - expectation maximization + Melanie Courtot + Ryan Brinkman + ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 + log-log curve fitting - + - - - global modularity calculation + + + feature extraction objective - A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. - Richard Scheuermann - PERSON: Richard Scheuermann - global modularity calculation - - - - - - - - - dye swap merge - - A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. - Elisabetta Manduchi + 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 James Malone - PERSON: Elisabetta Manduchi - PERSON: James Malone - dye swap merge + TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction + feature extraction objective - + - - + + + + - + - + - moving average - The moving average is often used to handle data from tiling arrays. + + + + + + + biexponential transformation + This type of transformation is typically used in flow cytometry. - 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. + A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. Elisabetta Manduchi - Helen Parkinson - Philippe Rocca-Serra - PERSON: Elisabetta Manduchi - PERSON: Helen Parkinson - moving average + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + biexponential transformation - + - + @@ -78445,413 +79392,391 @@ specified input and output of dt which were missing - replicate analysis - Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. + box-cox transformation - A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. - Elisabetta Manduchi - Helen Parkinson - PERSON: Helen Parkinson - PERSON:Elisabetta Manduchi - replicate analysis + A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. + Ryan Brinkman + ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. + box-cox transformation - + - - + + - + - b cell epitope prediction - - A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. - Helen Parkinson - PERSON: Helen Parkinson - b cell epitope prediction - - - - - + hyperlog transformation + This type of transformation is typically used in flow cytometry + + A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42." + http://flowcyt.sourceforge.net/gating/latest.pdf + hyperlog transformation + + - - - - - - - - - mhc binding prediction - - An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. - Helen Parkinson - PERSON: Helen Parkinson - mhc binding prediction + + + + + + loess scale group transformation one-channel + Loess scale group normalization applied to data from two one-channel expression microarray assays. + + A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. + Elisabetta Manduchi + OTHER: Editor's adjustment based on MGED Ontology term + loess scale group transformation one-channel - + - - + + - + - t cell epitope prediction - - A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. - Helen Parkinson - PERSON: Helen Parkinson - t cell epitope prediction + logical transformation + This type of transformation is typically used in flow cytometry. + + A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + logical transformation - + - - - data imputation + + + loess scale group transformation two-channel + Loess scale group normalization applied to data from a two-channel expression microarray assay. - Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. - Monnie McGee - ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. - data imputation + A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. + Elisabetta Manduchi + OTHER: Adjusted from MGED Ontology + loess scale group transformation two-channel - + - - - - - - - - - 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: Tina Hernandez-Boussard - PERSON: Tina Boussard - continuum mass spectrum + + + loess global transformation one-channel + Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. + + A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. + Elisabetta Manduchi + OTHER: Editor's generalization based on MGED Ontology term + loess global transformation one-channel - + - - - - - - - - - characteristic path length calculation - - Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices - PERSON: Tina Hernandez-Boussard - PERSON: Tina Hernandez-Boussard - characteristic path length calculation + + + split-scale transformation + This type of transformation is typically used in flow cytometry + + A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + split-scale transformation - + - - + + + loess global transformation two-channel + Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. + + A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. + Elisabetta Manduchi + OTHER: Editor's generalization based on MGED Ontology term + loess global transformation two-channel + + + + + + + + - + - centroid mass spectrum - - 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 - centroid mass spectrum + sine transformation + sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc. + + A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. + Elisabetta Manduchi + WEB: http://mathworld.wolfram.com/Sine.html + sine transformation - + - - - - - - - - - - - - - - + + - + - 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 - - 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 - Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method - Holm-Bonferroni family-wise error rate correction method + cosine transformation + cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc. + + 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 + WEB: http://mathworld.wolfram.com/Cosine.html + cosine transformation - + - - - edge weighting - - Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. - Tina Hernandez-Boussard - editor - was classified under algorithm class which is not acceptable super-class -TO BE DEALT WITH STILL BY RICHARD. JAMES - edge weighting + + + loess group transformation one-channel + A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. + + A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. + Elisabetta Manduchi + OTHER: Editor's generalization based on MGED Ontology term + loess group transformation one-channel - + - - - - - - - - - loess transformation + + + loess group transformation two-channel + A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. - A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. + A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra OTHER: Editor's generalization based on MGED Ontology term - loess transformation + loess group transformation two-channel - + - - - - - - - - - - - - - - - - - curve fitting data transformation + + + homogeneous polynomial transformation + a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables. - A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. + A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. Elisabetta Manduchi - James Malone - Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Curve_fitting - curve fitting data transformation + WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html + homogeneous polynomial transformation - + - - - - - - - - - + + - + - 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. - 2011-03-31: [PRS]. -creating a defined class by specifying the necessary output of dt -allows correct classification of FWER dt - 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 - family wise error rate correction method + linlog transformation + This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. + + 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 + PMID: 16646782 + linlog transformation - + - - - submatrix extraction - When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set. + + + + + + + + + variance stabilizing transformation + This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536. - A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) - Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix. + A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper. Elisabetta Manduchi James Malone Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Submatrix - submatrix extraction + variance stabilising transformation + PMID: 12169536 + variance stabilizing transformation - + - - - row submatrix extraction - When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set. + + + loess global transformation - A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. + A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. Elisabetta Manduchi James Malone Melanie Courtot - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - row submatrix extraction + Philippe Rocca-Serra + OTHER: Editor's generalization based on MGED Ontology term + loess global transformation - + - - - column submatrix extraction - When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set. + + + loess group transformation - A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. + A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. Elisabetta Manduchi James Malone Melanie Courtot - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - column submatrix extraction + Philippe Rocca-Serra + OTHER: Editor's generalization based on MGED Ontology term + loess group transformation - + - - - + + - + - - + + - gating - - Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. + loess scale group transformation + + A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. + Elisabetta Manduchi James Malone - Josef Spidlen Melanie Courtot - Richard Scheuermann - Ryan Brinkman - PERSON: James Malone - PERSON: Josef Spidlen - PERSON: Richard Scheuermann - PERSON: Ryan Brinkman - PERSON:Melanie Courtot - gating + OTHER: Editor's generalization based on MGED Ontology term + loess scale group transformation - + - - - descriptive statistical calculation objective + + + + + + + + + total intensity transformation single + This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). - A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. + A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. Elisabetta Manduchi + Helen Parkinson James Malone Melanie Courtot - Monnie McGee - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - PERSON: Monnie McGee - descriptive statistical calculation objective + 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 - + - + + + + + + + + + total intensity transformation paired + This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. + + 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 + 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 + + + + + + + - + - @@ -78866,211 +79791,172 @@ allows correct classification of FWER dt - - - - - - - - - - - - - - - + - arithmetic mean calculation - - 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 - 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) - arithmetic mean calculation + quantile transformation + This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. + + A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + quantile transformation - + - - - network analysis - - 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 - PERSON: Richard Scheuermann - network analysis - - - - - - - - - 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 - sequence analysis objective + + + + + + + + + mean centering + This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered. + + 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 + mean centring + PERSON: Elisabetta Manduchi + mean centering - + - - + + - + - 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 - longitudinal data analysis - longitudinal data analysis + median centering + This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered. + + 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 + median centring + PERSON: Elisabetta Manduchi + median centering - + - + - survival analysis objective - 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 - survival analysis objective + differential expression analysis objective + Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software + + A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + differential expression analysis objective - + - - + + + - + - - - mass spectrometry analysis + + K-fold cross validation method - A data transformation which has the objective of spectrum analysis. - mass spectrometry analysis + 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 - + - - + + + - + - - - spread calculation data transformation + + 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 - A spread calculation is a data transformation that has objective spread calculation. - James Malone - EDITOR - spread calculation data transformation + 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 - + - - + + - + - Kaplan Meier + jackknifing method + simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure - 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 + 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 + jackknifing 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 - 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. - multiple testing correction method - - - - - - - - - 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. + + 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. - 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 + 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 + boostrapping - + - - + + @@ -79080,67 +79966,38 @@ 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 - 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 - Westfall and Young FWER correction - Westfall and Young family wise error rate correction - - - - - - - - - polynomial transformation - a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 -variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables - - A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. - Elisabetta Manduchi - WEB: http://mathworld.wolfram.com/Polynomial.html - polynomial transformation - - - - - - - - - + - logarithmic transformation - - A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. - Elisabetta Manduchi - WEB: http://en.wikipedia.org/wiki/Logarithm - logarithmic transformation + 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) + + 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 + Philippe Rocca-Serra + Helen Parkinson + Benjamini and Hochberg false discovery rate correction method - + - + @@ -79148,183 +80005,186 @@ variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variabl - exponential transformation - - An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. + pareto scaling + + A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. Elisabetta Manduchi - WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function - WEB: http://en.wikipedia.org/wiki/Exponential_function - exponential transformation - - - - - - - - - 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 + Philippe Rocca-Serra + PMID:16762068 + pareto scaling - + - - - - - - - - - soft independent modeling of class analogy analysis + + + modular decomposition - 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. + Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. Tina Hernandez-Boussard - SIMCA - WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies - soft independent modeling of class analogy analysis + editor + modular decomposition - + - + - - + - + - + - - - - - - - discriminant function analysis - - Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. - Tina Hernandez-Boussard - WEB: http://www.statsoft.com/textbook/stdiscan.html - discriminant function analysis - - - - - - - - - - canonical variate analysis + k-means clustering - canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. - Tina Hernandez-Boussard - CVA - WEB: http://en.wikipedia.org/wiki/Canonical_analysis - canonical variate analysis + 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 + James Malone + Philippe Rocca-Serra + WEB: http://en.wikipedia.org/wiki/K-means + k-means clustering - + - + - - - + - + - - - - - - - linear discriminant functional analysis + hierarchical clustering - Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. - Tina Hernandez-Boussard - PERSON: Tina Hernandez-Boussard - linear discriminant functional analysis + A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). + James Malone + WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering + hierarchical clustering - + - - - regression analysis method + + + average linkage hierarchical clustering - Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. - Tina Hernandez-Boussard - BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 - regression analysis method + An average 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 average distance between objects from the first cluster and objects from the second cluster. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + average linkage hierarchical clustering - + - - - multiple linear regression analysis + + + complete linkage hierarchical clustering + + an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + complete linkage hierarchical clustering + + + + + + + + + single linkage hierarchical clustering - multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as - Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon -where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. - Tina Hernandez-Boussard - WEB:http://en.wikipedia.org/wiki/Linear_regression - multiple linear regression analysis + 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 + PERSON: Elisabetta Manduchi + single linkage hierarchical clustering - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + 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) + + 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 + Philippe Rocca-Serra + Helen Parkinson + Benjamini and Yekutieli false discovery rate correction method + + + + + + + - @@ -79340,120 +80200,135 @@ where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s - principal component regression - - The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. - Tina Hernandez-Boussard - WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html - principal component regression + dimensionality reduction + + A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. + Elisabetta Manduchi + James Malone + Melanie Courtot + Philippe Rocca-Serra + data projection + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + dimensionality reduction - + - - - partial least square regression analysis - - Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that -Y = b0 + b1X1 + b2X2 + ... + bpXp -In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. - Tina Hernandez-Boussard - PLS-RA - ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263. - partial least square regression analysis + + + principal components analysis dimensionality reduction + + A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. + Elisabetta Manduchi + James Malone + Melanie Courtot + Philippe Rocca-Serra + pca data reduction + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + principal components analysis dimensionality reduction - + - + - discriminant analysis - - Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. - Tina Hernandez-Boussard - WEB: http://www.statsoft.com/textbook/stdiscan.html - discriminant analysis + probabilistic algorithm + + A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. + James Malone + PERSON: James Malone + probabilistic algorithm - + - - - 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. + + + expectation maximization + + EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. James Malone - PLS-DA - WEB: http://www.camo.com/rt/Resources/pls-da.html - partial least square discriminant analysis + PERSON: James Malone + expectation maximization - + - - - - - - - - - eh transformation - This type of transformation is typically used in flow cytometry. + + + global modularity calculation + + A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. + Richard Scheuermann + PERSON: Richard Scheuermann + global modularity calculation + + + + + + + + + dye swap merge - An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. + A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - eh transformation + James Malone + PERSON: Elisabetta Manduchi + PERSON: James Malone + dye swap merge - + - - - + + - + - + - b transformation - This type of transformation is typically used in flow cytometry. + moving average + The moving average is often used to handle data from tiling arrays. - A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. + 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 - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - b transformation + Helen Parkinson + Philippe Rocca-Serra + PERSON: Elisabetta Manduchi + PERSON: Helen Parkinson + moving average - + - + @@ -79461,736 +80336,702 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - s transformation - This type of transformation is typically used in flow cytometry. + replicate analysis + Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. - An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. + A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - s transformation + Helen Parkinson + PERSON: Helen Parkinson + PERSON:Elisabetta Manduchi + replicate analysis - + - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - + + - 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 - visualization - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - PERSON: Tina Boussard - Possible future hierarchy might include this: -information_encoding ->data_encoding ->>image_encoding - data visualization + b cell epitope prediction + + A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. + Helen Parkinson + PERSON: Helen Parkinson + b cell epitope prediction - + - - - - - - - - - - + + - - + + - similarity calculation - - A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - similarity calculation + mhc binding prediction + + An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. + Helen Parkinson + PERSON: Helen Parkinson + mhc binding prediction - + - - - euclidean distance calculation - - An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - euclidean distance calculation + + + + + + + + + t cell epitope prediction + + A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. + Helen Parkinson + PERSON: Helen Parkinson + t cell epitope prediction - + - - - pearson correlation coefficient calculation + + + data imputation - A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - WEB: http://en.wikipedia.org/wiki/Correlation - pearson correlation coefficient calculation + Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. + Monnie McGee + ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. + data imputation - + - - + + - + - loess fitting - - 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 - ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. - loess fitting + 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: Tina Hernandez-Boussard + PERSON: Tina Boussard + continuum mass spectrum - + - - - - - - - - - - - - - - - - - - + + - + - mode calculation - - A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. - James Malone - Monnie McGee - PERSON: James Malone - PERSON: Monnie McGee - From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) - mode calculation + characteristic path length calculation + + Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices + PERSON: Tina Hernandez-Boussard + PERSON: Tina Hernandez-Boussard + characteristic path length calculation - + - - + + - + - quantile calculation - - A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. - Monnie McGee - WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html - quantile calculation + centroid mass spectrum + + 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 + centroid mass spectrum - + - - - - - - - - - - - - - - - - - - + + - - + + - median calculation - - A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values. - James Malone - Monnie McGee - PERSON: James Malone - PERSON: Monnie McGee - From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) - median calculation - - - - - - - - - - - + + - + - variance calculation + 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 - A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. - Monnie McGee - PERSON: Monnie McGee - From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008) - variance calculation + 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 + Philippe Rocca-Serra + WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method + Holm-Bonferroni family-wise error rate correction method - + - - - - - - - - - - - - - - - - standard deviation calculation - - A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. - Monnie McGee - PERSON: Monnie McGee - From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) - standard deviation calculation + + + edge weighting + + Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. + Tina Hernandez-Boussard + editor + was classified under algorithm class which is not acceptable super-class +TO BE DEALT WITH STILL BY RICHARD. JAMES + edge weighting - + - - - - - - - - - + + - + - interquartile-range calculation - - The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. - Monnie McGee - PERSON: Monnie McGee - From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) - interquartile-range calculation + loess transformation + + A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. + Elisabetta Manduchi + James Malone + Melanie Courtot + Philippe Rocca-Serra + OTHER: Editor's generalization based on MGED Ontology term + loess transformation - + - - - - - + + - + - + - + - + - - - - - - - - skewness calculation - - A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment - Monnie McGee - WEB: http://www.riskglossary.com/link/skewness.htm - From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) - skewness calculation + + + curve fitting data transformation + + A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. + Elisabetta Manduchi + James Malone + Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Curve_fitting + curve fitting data transformation - + - - - - + + - - + + - + + + - + - kurtosis calculation - - A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html - Monnie McGee - WEB: http://davidmlane.com/hyperstat/A53638.html - From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) - kurtosis calculation + 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. + 2011-03-31: [PRS]. +creating a defined class by specifying the necessary output of dt +allows correct classification of FWER dt + 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 + family wise error rate correction method - + - - - - - - - - - data combination - - 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 - editor - data combination + + + submatrix extraction + When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set. + + A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) + Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix. + Elisabetta Manduchi + James Malone + Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Submatrix + submatrix extraction - + - - - network graph construction - - A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. - Richard Scheuermann - PERSON: Richard Scheuermann - network graph construction + + + row submatrix extraction + When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set. + + A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. + Elisabetta Manduchi + James Malone + Melanie Courtot + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + row submatrix extraction - + - - - weighted network graph construction - - A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. - Richard Scheuermann - PERSON: Richard Scheuermann - weighted network graph construction + + + column submatrix extraction + When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set. + + A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. + Elisabetta Manduchi + James Malone + Melanie Courtot + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + column submatrix extraction - + - - - directed network graph construction + + + + + + + + + + + + + + + + gating - A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. + Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. + James Malone + Josef Spidlen + Melanie Courtot Richard Scheuermann + Ryan Brinkman + PERSON: James Malone + PERSON: Josef Spidlen PERSON: Richard Scheuermann - directed network graph construction + PERSON: Ryan Brinkman + PERSON:Melanie Courtot + gating - + - - - node quality calculation - - A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. - Richard Scheuermann - PERSON: Richard Scheuermann - node quality calculation + + + descriptive statistical calculation objective + + A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. + Elisabetta Manduchi + James Malone + Melanie Courtot + Monnie McGee + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + PERSON: Monnie McGee + descriptive statistical calculation objective - + - - - node degree calculation - - A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node. - Richard Scheuermann - PERSON: Richard Scheuermann - node degree calculation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + arithmetic mean calculation + + 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 + 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) + arithmetic mean calculation - + - - - quantitative node degree calculation + + + network analysis - A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. + 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 PERSON: Richard Scheuermann - quantitative node degree calculation + network analysis - + - - - node in-degree calculation - - A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node. - Richard Scheuermann - PERSON: Richard Scheuermann - node in-degree calculation + + + 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 + sequence analysis objective - + - - - node out-degree calculation - - A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. - Richard Scheuermann - PERSON: Richard Scheuermann - node out-degree calculation + + + + + + + + + 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 + longitudinal data analysis + longitudinal data analysis - + - - - node shortest path identification - - A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. - Richard Scheuermann - PERSON: Richard Scheuermann - node shortest path identification + + + survival analysis objective + 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 + survival analysis objective - + - - - edge quality calculation - - A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. - Richard Scheuermann - PERSON: Richard Scheuermann - edge quality calculation + + + + + + + + + mass spectrometry analysis + + A data transformation which has the objective of spectrum analysis. + mass spectrometry analysis - + - - - edge betweenness calculation - - An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. - Richard Scheuermann - PERSON: Richard Scheuermann - edge betweenness calculation + + + + + + + + + spread calculation data transformation + + A spread calculation is a data transformation that has objective spread calculation. + James Malone + EDITOR + spread calculation data transformation - + - - - network subgraph quality calculation - - A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. - Richard Scheuermann - PERSON: Richard Scheuermann - network subgraph quality calculation + + + + + + + + + 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 + Kaplan Meier - + - - - subgraph degree calculation - - A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - subgraph degree calculation + + + + + + + + + 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 + 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. + multiple testing correction method - - - - - quantitative subgraph degree calculation - - A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - quantitative subgraph degree calculation - - - + - + + + 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. - - - 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 - mathematical feature +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 + inter-rater reliability objective - + - - + + - - + + - 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 - log base + + + + + + + + + + + + + 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 + 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 + Westfall and Young FWER correction + Westfall and Young family wise error rate correction - + - - - subgraph in-degree calculation - - A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - subgraph in-degree calculation + + + polynomial transformation + a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 +variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables + + A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. + Elisabetta Manduchi + WEB: http://mathworld.wolfram.com/Polynomial.html + polynomial transformation - + - - - subgraph out-degree calculation - - A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - subgraph out-degree calculation + + + + + + + + + logarithmic transformation + + A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. + Elisabetta Manduchi + WEB: http://en.wikipedia.org/wiki/Logarithm + logarithmic transformation - - - - - intra subgraph connectivity calculation - - A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - intra subgraph connectivity calculation - - - - - - - - - subgraph modularity calculation - - A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. - Richard Scheuermann - PERSON: Richard Scheuermann - subgraph modularity calculation - - - - - - - - - network graph quality calculation - - A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole. - Richard Scheuermann - PERSON: Richard Scheuermann - network graph quality calculation - - - - - + - + @@ -80198,386 +81039,285 @@ information_encoding - unit-variance scaling - - A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. + exponential transformation + + An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. Elisabetta Manduchi - Philippe Rocca-Serra - autoscaling - PMID:16762068 - unit-variance scaling + WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function + WEB: http://en.wikipedia.org/wiki/Exponential_function + exponential transformation - + - + - 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 + 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 - + - - + + - - + + - exponential base + soft independent modeling of class analogy analysis - 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 + 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 + SIMCA + WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies + soft independent modeling of class analogy analysis - + - - + + + + + - - - - + + + + + + + + + + + + - 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 - polynomial degree - - - - - - - - - - + + - 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 - number of variables - - - - - - - - - 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 - James Malone - bottom-up hierarchical clustering - PERSON: Elisabetta Manduchi - agglomerative hierarchical clustering - - - - - - - - - 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 - James Malone - top-down hierarchical clustering - PERSON: Elisabetta Manduchi - divisive hierarchical clustering - - - - - - - - - data partitioning - - Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. - James Malone - PERSON: Melanie Courtot - PERSON: Richard Scheuermann - PERSON: Ryan Brinkman - data partitioning - - - - - - - - - data vector reduction objective + discriminant function analysis - 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 - Richard H. Scheuermann - PERSON: Richard H. Scheuermann - data vector reduction objective + Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. + Tina Hernandez-Boussard + WEB: http://www.statsoft.com/textbook/stdiscan.html + discriminant function analysis - + - - + + + - + - generalized family wise error rate correction method + canonical variate analysis - 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 - generalized family wise error rate correction method + canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. + Tina Hernandez-Boussard + CVA + WEB: http://en.wikipedia.org/wiki/Canonical_analysis + canonical variate analysis - + - + - + + + - + - + - quantile number of false positives correction method + + + + + + + linear discriminant functional analysis - 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 - quantile number of false positives correction method + Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. + Tina Hernandez-Boussard + PERSON: Tina Hernandez-Boussard + linear discriminant functional analysis - + - - - - - - - - - tail probability for the proportion of false positives correction method + + + regression analysis 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 - TPPFP correction method - 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 + Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. + Tina Hernandez-Boussard + BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 + regression analysis method - + - - - - - - - - - - - - - - - - - - - - - - false discovery rate correction method + + + multiple linear regression analysis - 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 - 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 - false discovery rate correction method + multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as + Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon +where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. + Tina Hernandez-Boussard + WEB:http://en.wikipedia.org/wiki/Linear_regression + multiple linear regression analysis - + - + - + + - + - + - proportion of expected false positives correction method + principal component regression - 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 - proportion of expected false positives correction method + The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. + Tina Hernandez-Boussard + WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html + principal component regression - + - - - - - - - - - - - - - - - - - - quantile proportion of false positives correction method + + + partial least square regression analysis - 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 - quantile proportion of false positives correction method + Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that +Y = b0 + b1X1 + b2X2 + ... + bpXp +In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. + Tina Hernandez-Boussard + PLS-RA + ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263. + partial least square regression analysis - + - - - data transformation objective - normalize objective - - An objective specification to transformation input data into output data - Modified definition in 2013 Philly OBI workshop - James Malone - PERSON: James Malone - data transformation objective + + + discriminant analysis + + Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. + Tina Hernandez-Boussard + WEB: http://www.statsoft.com/textbook/stdiscan.html + discriminant analysis - + - - - data normalization objective - Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. - - 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 + + + 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. James Malone - PERSON: Elisabetta Manduchi - PERSON: Helen Parkinson - PERSON: James Malone - data normalization objective + PLS-DA + WEB: http://www.camo.com/rt/Resources/pls-da.html + partial least square discriminant analysis - + - - - correction objective - Type I error correction - - 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 - correction objective + + + + + + + + + eh transformation + This type of transformation is typically used in flow cytometry. + + An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + eh transformation - + - - + + + + - + @@ -80586,237 +81326,197 @@ to create a common base for comparisons. - + - - - normalization data transformation - - A normalization data transformation is a data transformation that has objective normalization. - James Malone - PERSON: James Malone - normalization data transformation + + b transformation + This type of transformation is typically used in flow cytometry. + + A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + b transformation - + - - - - - - - - - - - - - - - - - averaging data transformation - - An averaging data transformation is a data transformation that has objective averaging. - James Malone - PERSON: James Malone - averaging data transformation - - - - - - - - + + + - + - - - partitioning data transformation - - A partitioning data transformation is a data transformation that has objective partitioning. - James Malone - PERSON: James Malone - partitioning data transformation - - - - - - - - - partitioning objective - A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. + + s transformation + This type of transformation is typically used in flow cytometry. - 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 - James Malone - PERSON: Elisabetta Manduchi - partitioning objective - - - - - - - - - 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 - James Malone - PERSON: Elisabetta Manduchi - background correction objective - - - - - - - - - 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 - James Malone - PERSON: Elisabetta Manduchi - curve fitting objective + An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + s transformation - + - - - - - - - - - - - - - - - - - class discovery data transformation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + data visualization + Generation of a heatmap from a microarray dataset - 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 + 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 + visualization + PERSON: Elisabetta Manduchi PERSON: James Malone - class discovery data transformation + PERSON: Melanie Courtot + PERSON: Tina Boussard + Possible future hierarchy might include this: +information_encoding +>data_encoding +>>image_encoding + data visualization - + - - + + + + - - + + - 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 - - - - - - - - - center calculation objective - A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. + + + + + + + similarity calculation - 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 - center calculation objective + A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + similarity calculation - + - - - class discovery objective + + + euclidean distance calculation - 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 - discriminant analysis objective - unsupervised classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone - class discovery objective + An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + euclidean distance calculation - + - - - class prediction objective + + + pearson correlation coefficient calculation - 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 - supervised classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone - class prediction objective + A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + WEB: http://en.wikipedia.org/wiki/Correlation + pearson correlation coefficient calculation - + - - - spread calculation objective - 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 - Awaiting English definition from Monnie McGee - James Malone - Person:Helen Parkinson - spread calculation objective + + + + + + + + + loess fitting + + 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 + ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. + loess fitting - + - - + + + + + - + @@ -80825,6674 +81525,6044 @@ 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 - PERSON: James Malone - center calculation data transformation - - - - - - - - - - - - - - - - - - - + - - - data vector reduction data transformation - - A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k. + + + + + + + + mode calculation + + A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. James Malone + Monnie McGee PERSON: James Malone - data vector reduction data transformation + PERSON: Monnie McGee + From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) + mode calculation - + - - - scaling objective - 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 - Awaiting English definition from Monnie McGee - James Malone - Person:Helen Parkinson - scaling objective + + + + + + + + + quantile calculation + + A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. + Monnie McGee + WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html + quantile calculation - + - - + + + + + - + - + - + - + - - - descriptive statistical calculation data transformation - - A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. - James Malone - PERSON: James Malone - descriptive statistical calculation data transformation - - - - - - - - + + - + - - - scaling data transformation - - A scaling data transformation is a data transformation that has objective scaling. + + median calculation + + A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values. James Malone + Monnie McGee PERSON: James Malone - scaling data transformation + PERSON: Monnie McGee + From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) + median calculation - + - - - error correction objective - 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 - error correction objective + + + + + + + + + + + + + + + + variance calculation + + A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. + Monnie McGee + PERSON: Monnie McGee + From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008) + variance calculation - + - - + + + + - + - - - sequence analysis data transformation - - 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 - sequence analysis data transformation + + + + + + + + standard deviation calculation + + A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. + Monnie McGee + PERSON: Monnie McGee + From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) + standard deviation calculation - + - - - cross validation objective - - 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 - cross validation objective + + + + + + + + + + + + + + + + interquartile-range calculation + + The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. + Monnie McGee + PERSON: Monnie McGee + From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) + interquartile-range calculation - + - - - 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 - merging objective - - - - - - - - + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + - - + + - 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 + skewness calculation + + A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment + Monnie McGee + WEB: http://www.riskglossary.com/link/skewness.htm + From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) + skewness calculation - + - - + + + - - + + - - + + - 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 + kurtosis calculation + + A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html + Monnie McGee + WEB: http://davidmlane.com/hyperstat/A53638.html + From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) + kurtosis calculation - + - - - - - - - - - - - - - - - + + - - + + - classified data visualization + data combination - 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 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 + editor + data combination - + - - - - - - - - - - - - - - - - - - - - - - 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 + + + network graph construction + + A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. + Richard Scheuermann + PERSON: Richard Scheuermann + network graph construction - + - - - - - - - - - survival analysis data transformation - - A data transformation which has the objective of performing survival analysis. - James Malone - PERSON: James Malone - survival analysis data transformation + + + weighted network graph construction + + A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. + Richard Scheuermann + PERSON: Richard Scheuermann + weighted network graph construction - + - - - - - - - - - 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 + + + directed network graph construction + + A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. + Richard Scheuermann + PERSON: Richard Scheuermann + directed network graph construction - + - - - 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 + + + node quality calculation + + A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. + Richard Scheuermann + PERSON: Richard Scheuermann + node quality calculation - + - - - 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 + + + node degree calculation + + A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node. + Richard Scheuermann + PERSON: Richard Scheuermann + node degree calculation - + - - - - - - - - - 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 + + + quantitative node degree calculation + + A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. + Richard Scheuermann + PERSON: Richard Scheuermann + quantitative node degree calculation - + - - - - - - - - - gas chromatography mass spectrometry - - 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 + + + node in-degree calculation + + A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node. + Richard Scheuermann + PERSON: Richard Scheuermann + node in-degree calculation - + - - - - - - - - - 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 + + + node out-degree calculation + + A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. + Richard Scheuermann + PERSON: Richard Scheuermann + node out-degree calculation - + - - - 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 + + + node shortest path identification + + A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. + Richard Scheuermann + PERSON: Richard Scheuermann + node shortest path identification - + - - - sequential design - PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs. + + + edge quality calculation - 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 + A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. + Richard Scheuermann + PERSON: Richard Scheuermann + edge quality calculation - + - - - observation design - PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. + + + edge betweenness calculation - 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 + An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. + Richard Scheuermann + PERSON: Richard Scheuermann + edge betweenness calculation - + - - - 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) - true + + + network subgraph quality calculation + + A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. + Richard Scheuermann + PERSON: Richard Scheuermann + network subgraph quality calculation - + - - - - - - - - - - - - - - - - - - - - - - - - pool of specimens - - 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 - pool of specimens + + + subgraph degree calculation + + A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + subgraph degree calculation - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chemical solution - 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 - liquid chemical solution - GROUP: OBI Biomaterial Branch - chemical solution + + + quantitative subgraph degree calculation + + A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + quantitative subgraph degree calculation - + - - - 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 - buffer role + + + 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 + mathematical feature - + - - - - - - - - + + - - + + - 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) - solvent role + 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 + log base - + - - - - - - - - - - - - - - - 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. + + + subgraph in-degree calculation - 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) - solute role + A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + subgraph in-degree calculation - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + subgraph out-degree calculation + + A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + subgraph out-degree calculation - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + intra subgraph connectivity calculation + + A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + intra subgraph connectivity calculation - + - - - obsolete_liver - PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. -AJR Am J Roentgenol. 1990 Jan;154(1):87-93. + + + subgraph modularity calculation - 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 - true + A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. + Richard Scheuermann + PERSON: Richard Scheuermann + subgraph modularity calculation - + - - - 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. + + + network graph quality calculation - 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 - true + A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole. + Richard Scheuermann + PERSON: Richard Scheuermann + network graph quality calculation - + - - - - - - - - - - - - - - - denatured polymer - - Is a polymer which has lost secondary or tertiary structure - PERSON: Alan Ruttenberg - http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 - denatured polymer + + + + + + + + + unit-variance scaling + + A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. + Elisabetta Manduchi + Philippe Rocca-Serra + autoscaling + PMID:16762068 + unit-variance scaling - + - - - - - - - - - - - - - - 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 + + + 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 - OBI Biomaterial - decapitated organism + PERSON: Elisabetta Manduchi + MA transformation - + - - + + - - + + - validated information - PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." + exponential base - 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 - validated information + 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 - + - - + + - - + + - curated information - PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. + polynomial degree - 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 - curated information + 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 - + - - + + + - - + + - - - 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 - randomized group participant role + + 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 + number of variables - + - - - - - - - - - - - - - - - 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 - OBI Biomaterial - methylated polymer + + + 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 + James Malone + bottom-up hierarchical clustering + PERSON: Elisabetta Manduchi + agglomerative hierarchical clustering - + - - - - - - - - - - - - - - - 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 - OBI Biomaterial - genetically modified organism + + + 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 + James Malone + top-down hierarchical clustering + PERSON: Elisabetta Manduchi + divisive hierarchical clustering - + - - - - - - - - - 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 - predicted data item + + + data partitioning + + Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. + James Malone + PERSON: Melanie Courtot + PERSON: Richard Scheuermann + PERSON: Ryan Brinkman + data partitioning - + - - - - - - - - - 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 - mean-centered data + + + 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 + Richard H. Scheuermann + PERSON: Richard H. Scheuermann + data vector reduction objective - + - - + + - - + + - 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 - edited document + 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 + gFWER correction + 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 - + - - + + + + - - - - - - - - - + + + + + + - - - 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 - dissolved material entity + + 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 + QNFP + 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 - + - - + + - + - extraction - nucleic acid extraction using phenol chloroform - - 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 - extraction + 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 + TPPFP correction method + 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 - + - - - + + - - + + - + + + - - + + - 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 - filtration - - - - - - - - - - - - - - - + - 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 - centrifugation + 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. . + 2011-03-31: [PRS]. +creating a defined class by specifying the necessary output of dt +allows correct classification of FDR dt + 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 + false discovery rate correction method - + - - + + + - - - - + + + + + + + + + + + + - 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. + proportion of expected false positives correction method - 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 - staining + 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 + proportion of expected false positives correction method - + - - - - - - - - - - - - - - + + + - - - - + + + + + + + + + + + + - 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 - washing + 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 + QPFP correction method + 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 - + - - - - - - - - - - - - - - - - - - - - - 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) - irradiation + + + data transformation objective + normalize objective + + An objective specification to transformation input data into output data + Modified definition in 2013 Philly OBI workshop + James Malone + PERSON: James Malone + data transformation objective - + - - - - - - - - - - - - - - - - - - - - - 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 - polymerization + + + data normalization objective + Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. + + 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 + James Malone + PERSON: Elisabetta Manduchi + PERSON: Helen Parkinson + PERSON: James Malone + data normalization objective - + - - - 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 - trypsination + + + correction objective + Type I error correction + + 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 + correction objective - + - - - - - - - - - - - - - - - - - - - - - - - - - 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 - enzymatic ligation + + + + + + + + + + + + + + + + + normalization data transformation + + A normalization data transformation is a data transformation that has objective normalization. + James Malone + PERSON: James Malone + normalization data transformation - + - - - - - - - - - - - - - - - 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 - storage + + + + + + + + + + + + + + + + + averaging data transformation + + An averaging data transformation is a data transformation that has objective averaging. + James Malone + PERSON: James Malone + averaging data transformation - + - - - + + - - - - - - - - - + + - - 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] - cell lysis + + + partitioning data transformation + + A partitioning data transformation is a data transformation that has objective partitioning. + James Malone + PERSON: James Malone + partitioning data transformation - + - - - - - - - - - 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 - electrocution + + + partitioning objective + 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 + James Malone + PERSON: Elisabetta Manduchi + partitioning objective - + - - - 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 - cervical dislocation + + + 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 + James Malone + PERSON: Elisabetta Manduchi + background correction objective - + - - - 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 - asphyxiation + + + 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 + James Malone + PERSON: Elisabetta Manduchi + curve fitting objective - + - - + + + + + + + + + + + + + + + + + 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 + PERSON: James Malone + class discovery data transformation + + + + + + + + - - + + - 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 - lethal injection - OBI Biomaterial - intentional overdosing + 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 - + - - - 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 - decapitation + + + center calculation objective + A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. + + 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 + center calculation objective - + - - - 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] - group randomization + + + class discovery objective + + 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 + discriminant analysis objective + unsupervised classification objective + PERSON: Elisabetta Manduchi + PERSON: James Malone + class discovery objective - + - - - 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 - - obsolete_activation - true + + + class prediction objective + + 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 + supervised classification objective + PERSON: Elisabetta Manduchi + PERSON: James Malone + class prediction objective - + - - - + + + spread calculation objective + 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 + Awaiting English definition from Monnie McGee + James Malone + Person:Helen Parkinson + spread calculation objective + + + + + + + + + + + + + + + + + + + + + + + center calculation data transformation + + A center calculation data transformation is a data transformation that has objective of center calculation. + James Malone + PERSON: James Malone + center calculation data transformation + + + + + + + + + + + + + + + + + + + + + + + data vector reduction data transformation + + A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k. + James Malone + PERSON: James Malone + data vector reduction data transformation + + + + + + + + + scaling objective + 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 + Awaiting English definition from Monnie McGee + James Malone + Person:Helen Parkinson + scaling objective + + + + + + + + + + + + + + + + + + + + + + + descriptive statistical calculation data transformation + + A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. + James Malone + PERSON: James Malone + descriptive statistical calculation data transformation + + + + + + + + - + - - 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 - immobilization + + + scaling data transformation + + A scaling data transformation is a data transformation that has objective scaling. + James Malone + PERSON: James Malone + scaling data transformation - + - - - + + + error correction objective + 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 + error correction objective + + + + + + + + - - - - - - - - - - - - + + - - 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 - nucleic acid hybridization + + + sequence analysis data transformation + + 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 + sequence analysis data transformation - + - - + + + cross validation objective + + 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 + cross validation 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 + merging objective + + + + + + + + - + - - - - - - - + + + + + + + - - + + + 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 + + + + + + + + - - + + - - + + - 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 - elution + 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 - + - - + + - - + + + + + + + + + - DNA Subtraction - 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 - DNA Subtraction + + + + + + + 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 - + - - - - - - - - + + - + + + + + + + + - 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 - document editing - - - - - - - - - - - - - - - + - 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 - prediction + 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 - + - - - validation - PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. + + + + + + + + + survival analysis data transformation - 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) - validation + A data transformation which has the objective of performing survival analysis. + James Malone + PERSON: James Malone + survival analysis data transformation - + - - - - - - - - + + - - + + - 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 - electroporation + 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 - + - - - 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 - digital curation + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + + + + + + + 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 - + - - + + - - + + - analog-to-digital converter - The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. + gas chromatography mass spectrometry - 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 + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - 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 + 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 - + - - - arc lamp - The Jablochkoff Candle + + + ANOVA - 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 + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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) + true - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + pool of specimens + + 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 + pool of specimens - + - - - BioSorter1000 - BioSorter 1000 at TSRI Flow Cytometry Core Facility + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + chemical solution + 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 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 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 + liquid chemical solution + GROUP: OBI Biomaterial Branch + chemical solution - + - - - 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 + + + 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 + buffer role - + - - - 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 + + + + + + + + + + + + + + + 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) + solvent role - + - - - 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 + + + + + + + + + + + + + + + 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) + solute role - + - - - Cell Lab Quanta SC + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + comet assay + PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. - 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 + 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 - + - - + + + - - + + - - + + - 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 + + + + + + + + + + + + + + + + + + + + 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 - + - - - 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 + + + 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 + + obsolete_liver + true - + - - - 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 + + + 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 + + obsolete_adipose tissue + true - + - - - 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 + + + + + + + + + + + + + + + denatured polymer + + Is a polymer which has lost secondary or tertiary structure + PERSON: Alan Ruttenberg + http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 + denatured polymer - + - - - 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 + + + + + + + + + + + + + + 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 + OBI Biomaterial + decapitated organism - + - - - 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 + + + + + + + + + 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 + validated information - + - - - 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 + + + + + + + + + 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 + curated information - + - - - + + - - + + - - 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 + + + 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 + randomized group participant role - + - - - 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 + + + + + + + + + + + + + + + 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 + OBI Biomaterial + methylated polymer - + - - - 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 + + + + + + + + + + + + + + + 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 + OBI Biomaterial + genetically modified organism - + - - - 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 + + + + + + + + + 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 + predicted data item - + - - - dichroic mirror - ViewLux Alexa 594 dichroic mirror + + + + + + + + + mean-centered data - 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 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 - + - - + + - - + + - 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 + 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 + edited document - + - - - 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 - - - - - - - - - dye laser - Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. + + + + + + + + + + + + + + + + + + + + dissolved material entity + Salt molecules that have been mixed into water - 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 material entity that has been going through a process of being put into solution + Person:Bjoern Peters + Philippe Rocca-Serra + dissolved material entity - + - - - FACS Calibur - ""FACS Calibur at TFL, BCCRC, Vancouver"" + + + + + + + + + extraction + nucleic acid extraction using phenol chloroform - 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 - - - - - - - - - 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 - - - - - - - - - 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 - - - - - - - - - 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 - - - - - - - - - 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 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 + extraction - + - - - 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 + + + + + + + + + + + + + + + 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 + filtration - + - - - 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 + + + + + + + + + + + + + + + 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 + centrifugation - + - - + + - - + + - 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 + 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 + staining - + - - + + - - + + - - + + - - + + + 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 + washing + + + + + + + + - - + + - - + + - - + + - 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 + 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) + irradiation - + - - - + + - - + + - - + + - 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 + + + + + + + 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 + polymerization - + - - - 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 + + + 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 + trypsination - + - - - Guava EasyCyte Mini + + + + + + + + + + + + + + + + + + + + + + + + + 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. - 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 + 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 + enzymatic ligation - + - - - 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 + + + + + + + + + + + + + + + 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 + storage - + - - - 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 + + + + + + + + + + + + + + + + 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] + cell lysis - + - - - 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 + + + + + + + + + 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 + electrocution - + - - - 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 + + + 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 + cervical dislocation - + - - - 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 + + + 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 + asphyxiation - + - - + + - - + + - - - - - - - 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 + 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 + lethal injection + OBI Biomaterial + intentional overdosing - + - - - 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 + + + 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 + decapitation - + - - - 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 + + + 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] + group randomization - + - - - interrogation_point - Interrogation point in BD FACS Calibur - - Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point. - John Quinn - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11 - interrogation_point + + + 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 + + obsolete_activation + true - + - - - 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 + + + + + + + + + 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 + immobilization - + - - - jet_in_air_flow_chamber - Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter - - A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air. - John Quinn - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - jet_in_air_flow_chamber + + + + + + + + + + + + + + + + + + + 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 + nucleic acid hybridization - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + elution - + - - - LactoScope C4 - LactoScope C4 Automatic Economical + + + + + + + + + DNA Subtraction + 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 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 material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. + Philippe Rocca-Serra + OBI-Branch + DNA Subtraction - + - - - 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 + + + + + + + + + + + + + + + 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 + document editing - + - - + + - - + + - 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 + + + + + + + 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 + prediction - + - - - 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 + + + 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) + validation - + - - - 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 + + + + + + + + + + + + + + + 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 + electroporation - + - - - 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 + + + 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 + digital curation - + - + - Luminex 100 + A10-Analyzer - 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. + 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.luminexcorp.com/products/luminex_100IS.html - Luminex 100 + http://www.apogeeflow.com/flow_cytometry_products.htm + A10-Analyzer - + - + - Luminex 200 + A40-MiniFCM - 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 + 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.luminexcorp.com/support/faqs.html - Luminex 200 + http://www.apogeeflow.com/flow_cytometry_products.htm + A40-MiniFCM - + - - - MACS Quant + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + flow cytometer analyzer + FACS Calibur, Luminex 100 - 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. + 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.miltenyi.com - MACS Quant + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + flow cytometer analyzer - + - - - metal vapor laser - Gold vapor laser, Helium-cadmium metal-vapor laser + + + arc lamp + The Jablochkoff Candle - 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. + 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 - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - metal vapor laser + http://en.wikipedia.org/wiki/Arc_lamp + arc lamp - + - + - mixed argon-krypton gas laser - argon-krypton laser in a cytometer + argon ion laser + argon ion 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 + 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 - + - - - 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. + + + 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 - http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16 - MoFlo + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + avalanche photodiode - + - - - multi-well plate - 96 well plate, 48 multiwell plate - - A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader. - FG this is synonymous with microtiter plate - John Quinn - http://www.nuncbrand.com/page.aspx?ID=301 - multi-well plate - - - - - - - - - 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 + + + 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 - + - - - - - - - - - obscuration bar - obscuration bar in a flow cytometer + + + band pass filter + 530/30 BP filter, 585/42 BP filter - 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 + 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 - + - - - - - - - - - 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. + + + 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://en.wikipedia.org/wiki/Optical_filter - optical filter + http://www.unionbio.com/products/BioSorter.html + BioSorter1000 - + - - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - + - - - particle delivery vessel - FC 500 particle delivery vessel - - Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - FG: this should be delted - particle delivery is a role that an object can play - particle delivery vessel + + + 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 - + - - - - - - - - - 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. + + + 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://einstein.stanford.edu/content/glossary/glossary.html - photodetector + http://www.unionbio.com/products/BioSorter.html + BioSorter500 - + - - - 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. + + + 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://cyto.mednet.ucla.edu/Protocols/flow.htm - photodiode + http://www.beckmancoulter.com/cell-lab + Cell Lab Quanta SC - + - - - - - - - - - + + - + - + - photomultiplier tube - R9647 by manufactured by Hamamatsu + charge plate + LSR2 charge plate - 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. + 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 - http://cyto.mednet.ucla.edu/Protocols/flow.htm - photomultiplier tube + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + charge plate - + - - - - - - - - - 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 - piezo electric crystal + + + 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 - + - - - - - - - - - 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. + + + 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.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf - plate loader + http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm + Cyan - + - - - 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. + + + 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 - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - preamplifier + http://www.partec.de/products/cyflow-ml.html + CYFlow ML - + - - - 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. + + + 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.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - quartz cuvette flow chamber + http://www.partec.de/products/cyflow.html + CyFlow SL - + - - - Reflection - Reflection at TSRI Flow Cytometry Core Facility + + + CyFlow SL3 - 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. + 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.i-cyt.com/reflection.htm - Reflection + http://www.partec.de/products/cyflowsl3.html + CyFlow SL3 - + - - - 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. + + + 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 - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - cytometer sample tube + http://www.partec.de/products/cyflowspace.html + CyFlow Space - + - - - - - - - - + + - - + + - 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 + 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 - + - - - 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. + + + 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://en.wikipedia.org/wiki/Low-pass_filter - short pass filter + http://www.cytobuoy.com/ + CytoSence - + - - - 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 + + + 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 - + - - - 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. + + + 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://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575 - Somacount + http://en.wikipedia.org/wiki/Dichroic_filter + dichroic filter - + - - - SomaScope - SomaScope Mark II Automatic Economical + + + dichroic mirror + ViewLux Alexa 594 dichroic mirror - 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 + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - 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. + 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 - Melanie Courtot - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - flow cytometer sorter + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + differential pressure gauge - + - - - - - - - - - - - - - - - syringe pump - NE-1000 Single Syringe Pump + + + diode laser + FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc. - 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 + 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 - + - - - - - - - - - voltage amplifier - Linear amplifier, log amplifier, microwave amplifier + + + dye laser + Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. - A voltage amplifier is a device that amplifies the voltage signal. - Frank Gibson - John Quinn - http://en.wiktionary.org/wiki/amplifier - voltage amplifier + 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 - + - - - - - - - - - waste tank - LSR2 waste tank + + + FACS Calibur + ""FACS Calibur at TFL, BCCRC, Vancouver"" - 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 + 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 - + - - - - - - - - - DNA sequencer - ABI 377 DNA Sequencer, ABI 310 DNA Sequencer + + + FACS Canto - A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. - Trish Whetzel - MO - DNA sequencer + 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 - + - - - - - - - - - - - - - - - array scanner - GenePix 4200A, GenePix4000B + + + FACS Canto2 - 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 + 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 - + - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - centrifuge + + + FACSAria + FACSAria at TSRI Flow Cytometry Core Facility - 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 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 - + - - - - - - - - - computer - Apple PowerBook, Dell OptiPlex + + + FACSvantage + FACSvantage at TSRI Flow Cytometry Core Facility - 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 + 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 - + - - - - - - - - - heating block - An instrument used to heat and/or maintain material at a set temperature. + + + FC 500 - 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 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 - + - - + + - + - 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 + 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 - + - - + + - - + + - - + + - 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 - - - - - - - - - + - - + + - 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 - - - - - - - - - - + + - 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 + + + + + + + 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 - + - + + - + - + - oligonucleotide synthesizer - Automated Multiplex Oligonucleotide Synthesizer - - An instrument used to chemically synthesize oligonucleotides. - Trish Whetzel - MO - oligonucleotide synthesizer + 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 - + - - - - - - - - - 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 + + + 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 - + - - - - - - - - - spectrophotometer - Helios Gamma Spectrophotometer + + + Guava EasyCyte Mini - 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 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 - + - - - - - - - - - - - - - - - thermal cycler - Piko(tm) 96-well Thermal Cycler + + + Guava EasyCyte Plus - 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 + 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 - + - - - - - - - - - - - - - - - - - - - - - vacuum dryer - Model 777 Microarray Oven + + + Guava Personal Cell Analysis - An instrument which removes liquid by the application of negative pressure, i.e. vacuum. - Trish Whetzel - MO - vacuum dryer + 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 - + - - - - - - - - - vortexer - VWR Genie 2 + + + Guava Personal Cell Analysis-96 - 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 + 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 - - - - - - - - - - - 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 - - - + - - - - - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - - molecular crosslinker - Stratalinker + + + helium neon ion laser + A helium neon laser can by used to irradiate cells in a flow cytometer. - 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 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 - + - - - - - - - - + + - + - - - - - - - + - image cytometer - The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. + Amnis ImageStream - An image_cytometer is an instrument for image-based study or measurement of cells. + 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://web.mit.edu/solab/Research/ImageCytometry.html - image cytometer + http://www.amnis.com/ + Amnis ImageStream - + - - - - - - - - - - - - - - - - - - - - - - - - - - - cytometer + + + inFlux Analyzer - A cytometer is an instrument for counting and/or measuring characteristics of cells. - Melanie Courtot - http://medical.merriam-webster.com/medical/cytometer - cytometer + 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 - + - - - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - 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 + + + interrogation_point + Interrogation point in BD FACS Calibur + + Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point. + John Quinn + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11 + interrogation_point - + - - - 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 + + + 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 - + - - - - - - - - - - - - - - - - - - - - - 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 + + + jet_in_air_flow_chamber + Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter + + A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air. + John Quinn + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + jet_in_air_flow_chamber - + - - - 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. + + + 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 - PERSON: Chris Stoeckert - microarray + John Quinn + krypton ion laser - + - - - 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 + + + 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 - + - - - 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. + + + 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 - PERSON: Daniel Schober - protein microarray + light amplification by the stimulated emission of radiation + John Quinn + http://en.wikipedia.org/wiki/Laser + laser - + - - + + - + - droplet sorter + light source - 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 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - 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 + + + 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 - + - - - - - - - - - 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 + + + 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 - + - - - - - - - - - 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. + + + 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 + + + + + + + + + MoFlo + MoFlo at TSRI Flow Cytometry Core Facility - 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 + 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 - + - - - 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 + + + multi-well plate + 96 well plate, 48 multiwell plate + + A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader. + FG this is synonymous with microtiter plate + John Quinn + http://www.nuncbrand.com/page.aspx?ID=301 + multi-well plate - + - - - 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 + + + 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 - + - - - 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 + + + + + + + + + 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 - + - - - 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 + + + + + + + + + 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 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + 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 - + - - - 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 + + + particle delivery vessel + FC 500 particle delivery vessel + + Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + FG: this should be delted - particle delivery is a role that an object can play + particle delivery vessel - + - - - 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 + + + + + + + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - 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 + + + + + + + + + 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 + piezo electric crystal - + - - - 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 + + + + + + + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + + + + + + + + + + + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 - - - - - - - - - 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 - - - - - - - - - stopping rule - PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy. - - a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen - PRS - PRS - stopping rule - - - - - - - - - compliance rule - - a compliance rule is a rule which ensures a compliance process occurs - PRS - PRS - compliance rule - - - - - - - - - standard compliance rule - - a standard compliance rule is a compliance rule which defines conformity to a representation standard - PRS - PRS - standard compliance rule - - - - - - - - - ethical standard compliance rule - - an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur - PRS - PRS - ethical standard compliance rule - - - - - - - - - eligibility criterion - PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. + + + Somacount - an eligibility criterion (rule) is_a selection criterion which -defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. - - Person: Philippe Rocca-Serra - eligibility rule - Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group - eligibility criterion + 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 - + - - - inclusion criterion - PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) . - - an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. - Person: Philippe Rocca-Serra - inclusion condition - inclusion rule - Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group - inclusion criterion + + + 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 - + - - - exclusion rule - PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. - - an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study - Person: Philippe Rocca-Serra - Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group - exclusion criterion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - - + + + 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 + + + + + + + + - - + + - adding substance to cell culture - 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 - Bjoern Peters - IEDB - adding substance to cell culture + 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 - + - - + + - - + + + 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 + + + + + + + + - - - - - - - + + - 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 + 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 - + - - + + - - + + - - - - - - - - - - - - + + + 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 + + + + + + + + - - + + - performing a clinical assessment + arrayer + BioRobotics Microgrid II TAS, Affymetrix GMS 417 - 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 - performing a clinical assessment + A device which deposits biological material onto a substrate in a defined pattern. + Trish Whetzel + MO_697 arrayer + arrayer - + - - + + + - - - - - - - - + + - - - - - - - - - - - - + + - + - - - - - - - - - + - - + + - human subject enrollment - enlisting familiy members of HIV patients into a study + centrifuge - 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 - Bjoern Peters - IEDB - criteria come from plan / clinical trial branch - human subject enrollment + 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 - + - - + + - - + + + 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 + + + + + + + + - - + + + 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 + + + + + + + + - - + + - collecting specimen from organism - taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient + homogenizer + mortar, blender - a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation - PERSON:Bjoern Peters - IEDB - collecting specimen from organism + 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 - + - - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - - - - - - - killing - Terminal sacrifice of animals by cervical dislocation at the end of an investigation. - - 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 - death status type - euthanisia - life termination - sacrifice - CEBS, Biomaterial_branch - killing + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - - + + + 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 + + + + + + + + - - 1 + + - administering substance in vivo - 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 - 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 - IEDB - administering substance in vivo + 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 - + - - + + - - - - - - - + + - - - - - - - - - + + - acquisition - Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. + oligonucleotide synthesizer + Automated Multiplex Oligonucleotide Synthesizer - the planned process of gaining possession of a continuant - 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' - Bjoern Peters - IEDB - This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition - acquisition + An instrument used to chemically synthesize oligonucleotides. + Trish Whetzel + MO + oligonucleotide synthesizer - + - - - exposure of material to environment - Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. - - a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. - Bjoern Peters - IEDB - Alan says there will be problmes, e.g. with selection by survival - exposure of material to environment + + + + + + + + + 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 - + - - + + - - + + - material acquisition - 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. + spectrophotometer + Helios Gamma Spectrophotometer - 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 - This excludes processes that create or change materials, such as material transformations. - Bjoern Peters, Alan Ruttenberg, Helen Parkinson - material procurement - IEDB - material acquisition + 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 - + - - - acclimatization - placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress - - A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. - Jennifer Fostel - CEBS, Biomaterial_branch - acclimatization + + + + + + + + + + + + + + + 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 - + - - + + - - + + - - + + - - + + - environmental material collection - Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas - - environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer. - relabel the term and add axiom connecting to EnVO:'environmental material' -discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/ - Bjoern Peters, Alan Ruttenberg - IEDB - the researcher is very interested in the location - environmental material collection process + 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 - + - - + + - - + + - information acquisition - Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC + vortexer + VWR Genie 2 - 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 - OBI branch derived - information acquisition + 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 - + - - + + + - - + + - - + + 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 + + + + + + + + - - + + - - + + - material component separation - Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification - - a material processing in which components of an input material become segregated in space - Bjoern Peters - IEDB - material component separation + 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 - + - - + + + - - + + - - - - - - - - - - - - + + - group assignment - Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation - - 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 - OBI Plan - group assignment + 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 - + - - + + - - + + - - + + - - + + - - 2 + + - 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 - PlanAndPlannedProcess Branch - sample pooling - OBI branch derived - like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. - pooling specimens + 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 - + - - + + - - + + - - + + - - - - - - - + + - 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 + + + + + + + cytometer + + A cytometer is an instrument for counting and/or measuring characteristics of cells. + Melanie Courtot + http://medical.merriam-webster.com/medical/cytometer + cytometer - + - - + + - - + + - material portioning - pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock + + + + + + + gel tank + CHEF gel box, slab gel box, capillary electrophoresis - a material processing in which the input substance is partitioned into a number of portions that are similar in composition. - PERSON:Bjoern Peters - aliquoting - apportioning - OBI branch derived - material portioning + 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 - + - - - non-specific labeling - The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. + + + + + + + + + power supply + A AC/DC transformer that generates the reqired power for an electrophoresis apparatus - The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial - PlanAndPlannedProcess Branch - OBI branch derived - definition blessed by Allyson, Bjoern, Jay & Randi - non-specific labeling + 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 - + - - + + + 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 + + + + + + + + - + - - + + - - - - - - - - - - - - - - + + - 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 + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cell fixation - http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus - - a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time - should include capturing what qualities are being preserved - PERSON:Bjoern Peters - OBI branch derived - we could generalize this for other input materials - cell fixation + + + 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 - + - - - - - - - - - excision - Cutting out the portion of a gel which contains a DNA fragment - - the use physical means to remove a portion of a substance from the rest - Alan Ruttenberg, Kevin Clancy - www.crohnsresource.com/glossary.jsp (via google define:resection) - excision + + + 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 - + - - - - non specific enzymatic cleavage - The use of agarase to digest an agar gel - - an enzymatic cleavage that uses an enzyme without a strong affinity for specific cleavage sites in the input material - PERSON:Kevin Clancy - OBI branch derived - non specific enzymatic cleavage + + + 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 - + - - - - - - - - - - - - - - - - - - - - - + + - - + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + - - + + - maintaining cell culture - When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture - - a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing - PlanAndPlannedProcess Branch - OBI branch derived - maintaining cell culture + 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 - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - + + - substance detection assay - the detection of phycoerytherin by means of flow cytometry + 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. - An assay that detects a specified substance - Kevin Clancy - OBI branch derived - substance detection assay + 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 - + - - + + - - + + - - + + - 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 + 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 - + - - + + - - + + - artificially induced cell membrane lysis - http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent. - - a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate - ---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined. - PlanAndPlannedProcess Branch - OBI branch derived - artificially induced cell membrane lysis + 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 - + - - - - - - - - - - - - - - - - - - - - + + - - + + - artificially induced reverse transcription - 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. - 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 - artificially induced reverse transcription + 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 - + - - + + - - + + - isolation of cell culture supernatant - Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube. - - a protocol which results in the separation of supernatant material from a cell culture - This does not apply to the case where the cells are lysed - PlanAndPlannedProcess Branch - OBI branch derived - isolation of cell culture supernatant + 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 + experimental design + rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. + + study design - + - - - - - - - - - experimental disease induction - the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome. + + + 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. - a protocol application to induce a specific disease in an organism - PlanAndPlannedProcess Branch - OBI branch derived - could be defined class - experimental disease induction + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. + + + 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 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 - - - - - - - - - - - - - - - artificially induced DNA repair - the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands - - a protocol application to repair damaged DNA molecules - PlanAndPlannedProcess Branch - OBI branch derived - ---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi - artificially induced DNA repair + 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 - + - - - - - - - - - - - - - - - - - - - - - cell permeabilization - Electroporation of HeLa cells to allow transfection with pUC19. + + + 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 protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application - need to add output cell has_quality permeable - PERSON:Bjoern Peters - OBI branch derived - definition blessed by Jay, Alan, Randi - cell permeabilization + 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 - + - - - - - - - - - precipitation - The use of ethanol to precipitate DNA molecules from a solution containing DNA + + + n-to-1 design - a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate) - PERSON:Kevin Clancy - OBI branch derived - precipitation + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - 'establishing cell culture' - - a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). - PERSON:Matthew Brush - PERSON:Matthew Brush - A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. - establishing cell culture + + + 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 - + - - - - - - - - - - - - - - - - - - - - - cell culture splitting - The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. + + + 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. - 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 - 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 + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - addition of molecular label - The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. + + + 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 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 - OBI developer call, 3-12-12 - addition of molecular label + 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 - + - - - - - - - - - artificially induced methylation - the use of enzymes to add methyl groups to DNA molecules + + + 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. - A planned process of adding methyl groups to polymers - PERSON:Kevin Clancy - OBI branch derived - artificially induced methylation + 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 - + - - - - - - - - - - - - - - - - - - - - - synthesis - making cDNA from nucleotides using RNA as a template + + + loop design + PMID: 12933549 - the construction of a biomaterial from simpler biomaterials - This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription - PERSON:Kevin Clancy - synthesize - OBI branch derived - synthesis + 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 - + - - - - - - - - - concentrate - Evaporation of the solution containing DNA to increase the concentration of the DNA molecules + + + reference design + PMID: 12933549 - a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material - PERSON:Kevin Clancy - OBI branch derived - concentrate + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - recombinant plasmid cloning - The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35. + + + 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. - the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial - PERSON:Kevin Clancy - OBI branch derived - recombinant plasmid cloning + 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 - + - - - - - - - - - - - - - - - genetic transformation - The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 - - the introduction. alteration or integration of genetic material into a cell or organism - PERSON:Kevin Clancy - genetic modification - OBI branch derived - genetic transformation + + + 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 - + - - - - - - - - - - lavage - the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present - - A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid - This is not washing, in which case the material of interest is not the resulting fluid - PlanAndPlannedProcess Branch - OBI branch derived - lavage + + + 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 - + - - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - preparative chromatography - The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides. + + + 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 + + + + + + + + + fractional factorial design - the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity - PERSON:Kevin Clancy; Bjoern Peters - OBI branch derived - preparative chromatography + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sequencing assay - The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template + + + 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 assay the uses chemical or biochemical means to infer the sequence of a biomaterial - PlanAndPlannedProcess Branch - OBI branch derived - sequencing assay + 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 - + - - - vector mediated amplification - E coli expressing the gene for M avium p35 were cultured in order to produce p35. + + + replicate design - The process of creating a copy of some biological entity in cell culture - PERSON:Kevin Clancy - OBI branch derived - vector mediated amplification + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - DNA polymerase amplification - The use of taq polymerase to amplify a DNA fragment during a PCR. + + + 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. - 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 - OBI branch derived - DNA polymerase amplification + 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 - + - - - specific enzymatic cleavage - The use of a protease to digest a protein into peptides + + + 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. - an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material - PERSON:Kevin Clancy - OBI branch derived - specific enzymatic cleavage + Groups of assays that are related as part of a time series. + Philippe Rocca-Serra on behalf of MO + MO_887 + time series design - + - - - - - - - - - gradient separation - the use of a sucrose gradient to isolate mitochondria + + + stopping rule + PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy. - a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities - PERSON:Kevin Clancy - OBI branch derived - gradient separation + a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen + PRS + PRS + stopping rule - + - - - - - - - - - dialysis - the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage + + + compliance rule - a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition - PERSON:Kevin Clancy - OBI branch derived - dialysis + a compliance rule is a rule which ensures a compliance process occurs + PRS + PRS + compliance rule - + - - + + + standard compliance rule + + a standard compliance rule is a compliance rule which defines conformity to a representation standard + PRS + PRS + standard compliance rule + + + + + + + + + ethical standard compliance rule + + an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur + PRS + PRS + ethical standard compliance rule + + + + + + + + + eligibility criterion + PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. + + an eligibility criterion (rule) is_a selection criterion which +defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. + + Person: Philippe Rocca-Serra + eligibility rule + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group + eligibility criterion + + + + + + + + + inclusion criterion + PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) . + + an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. + Person: Philippe Rocca-Serra + inclusion condition + inclusion rule + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group + inclusion criterion + + + + + + + + + exclusion rule + PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. + + an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study + Person: Philippe Rocca-Serra + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group + exclusion criterion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + - - + + - - + + - electrophoresis - Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change. + adding substance to cell culture + adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient - a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge - PERSON:Kevin Clancy - OBI branch derived - Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers. - electrophoresis + 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 + Bjoern Peters + IEDB + adding substance to cell culture - + - - + + - - + + - selection by survival - The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected + + + + + + + + + + + + tumor grading - the use of environmental conditions to select for the organism or cells that have a certain trait - PERSON:Kevin Clancy - OBI branch derived - selection by survival + 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 - + - - + + - - + + - DNA cleavage, restriction analysis - the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components - - A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence - PERSON:Kevin Clancy - restriction enzyme assay - DNA restriction enzyme digestion - - - - - - - - - + - - + + @@ -87502,50 +87572,51 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - protease cleavage - the use of trypsin to cleave pepsin into peptide fragments - - protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). - enzymatic digestion - PlanAndPlannedProcess Branch - OBI branch derived - protease cleavage - - - - - - - - - enzymatic DNA replication - the use of enzymes to duplicate DNA molecules - - the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial - PERSON:Kevin Clancy - OBI branch derived - enzymatic DNA replication + 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 + performing a clinical assessment - + - - + + + + + + + + + + + + + + + + + + + - + - - + + @@ -87554,542 +87625,27146 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + + + + + + + + + - + - - - - - - - enzymatic amplification - the use of a polymerase chain reaction to amplify a fragment of DNA - - the use of enzymes to increase the number of molecules of a biomaterial - PERSON:Kevin Clancy - OBI branch derived - enzymatic amplification + human subject enrollment + 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 + Bjoern Peters + IEDB + criteria come from plan / clinical trial branch + human subject enrollment - + - - + + - + - DNA transduction - The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein - - a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism - PERSON:Kevin Clancy - OBI branch derived - DNA transduction + + + + + + + + + + + + + collecting specimen from organism + taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient + + a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation + PERSON:Bjoern Peters + IEDB + collecting specimen from organism - + - - + + - + - - + + - DNA transfection - The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest - - a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell - PERSON:Kevin Clancy - OBI branch derived - DNA transfection - - - - - - - - - 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. - - 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 - PlanAndPlannedProcess Branch - OBI branch derived - vector mediated expression - - - - - - - - - - - - - - - - - - - - - + - + - - + + - - - - - - - recombinant vector cloning - - 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 - OBI branch derived - recombinant vector cloning - - - - - - - - - obsolete_defined processes - - Place holder class, see editor note - PlanAndPlannedProcess Branch - OBI branch derived - - obsolete_defined processes - true - - - - - - - - - specific labeling - The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells - - a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material - PlanAndPlannedProcess Branch - OBI branch derived - definition blessed by Allyson, Bjoern, Jay & Randi - specific labeling - - - - - - - - - - - - - - - RNA extraction + killing + Terminal sacrifice of animals by cervical dislocation at the end of an investigation. - A RNA extraction is a nucleic acid extraction where the desired output material is RNA - PlanAndPlannedProcess Branch - OBI branch derived - requested by Helen Parkinson for MO - RNA extraction + 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 + death status type + euthanisia + life termination + sacrifice + CEBS, Biomaterial_branch + killing - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + - + - nucleic acid extraction - Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. - - a material separation to recover the nucleic acid fraction of an input material - PlanAndPlannedProcess Branch - OBI branch derived - requested by Helen Parkinson for MO. Could be defined class - nucleic acid extraction - - - - - - - - - - + + - - + + 1 - cell culture supernatant - solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. -Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615 - - Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell. - PERSON: Bjoern Peters - GROUP: IEDB - cell culture supernatant + administering substance in vivo + 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 + 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 + IEDB + administering substance in vivo - + - - + + - - + + + + + + + - + - - + + - cell pellet - Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214 - - 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 - GROUP: CEBS - GROUP: OBI Biomaterial Branch - cell pellet + acquisition + 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. + 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' + Bjoern Peters + IEDB + This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition + acquisition - + - - - - - - - - - - - - - - - phage display library - PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] - - a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra - display library - WEB: http://www.immuneepitope.org/home.do - PRS: 22022008. class moved under population, -modification of definition and replacement of biomaterials in previous definition with 'material' -addition of has_role restriction - phage display library + + + exposure of material to environment + Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. + + a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. + Bjoern Peters + IEDB + Alan says there will be problmes, e.g. with selection by survival + exposure of material to environment - + - - - - - - - - + + - - + + - 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 + material acquisition + 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 + This excludes processes that create or change materials, such as material transformations. + Bjoern Peters, Alan Ruttenberg, Helen Parkinson + material procurement + IEDB + material acquisition + + + + + + + + + acclimatization + placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress - 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 - GROUP: PSI - cell lysate + A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. + Jennifer Fostel + CEBS, Biomaterial_branch + acclimatization - + - - + + - - + + - - + + - peptide construct - Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin - -A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617 - - a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion - PERSON: Bjoern Peters + + + + + + + environmental material collection + Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas + + environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer. + relabel the term and add axiom connecting to EnVO:'environmental material' +discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/ + Bjoern Peters, Alan Ruttenberg IEDB - peptide construct + the researcher is very interested in the location + environmental material collection process - + - - + + - - + + - transgenic organism - HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein -Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162 - - 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 - GROUP:IEDB - transgenic organism + information acquisition + Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC + + 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 + OBI branch derived + information acquisition - + - - - - + + + + + + + + - - + + - - + + - whole mount tissue - - 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 - whole mount sample - GROUP: OBI - PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity - PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application - whole mount tissue + material component separation + Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification + + a material processing in which components of an input material become segregated in space + Bjoern Peters + IEDB + material component separation - + - - - assay bead - Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. - - A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. - DS: Probably better modeled as a role. - OBI - bead - assay bead + + + + + + + + + + + + + + + + + + + + + + + + + group assignment + Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation + + 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 + OBI Plan + group assignment - + - - + + + - - + + - - - epitope - - a material entity bearing the epitope role - IEDB - IEDB - epitope + + + + + + + + + + + + + + + + + 2 + + + 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 + PlanAndPlannedProcess Branch + sample pooling + OBI branch derived + like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. + pooling specimens - + - - - obsolete_occurrence of disease + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + material portioning + pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock - An occurrence of disease is a process involving pathologic changes within an organism - IEDB - IEDB - - obsolete_occurrence of disease - true + a material processing in which the input substance is partitioned into a number of portions that are similar in composition. + PERSON:Bjoern Peters + aliquoting + apportioning + OBI branch derived + material portioning + + + + + + + + + non-specific labeling + The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. + + The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial + PlanAndPlannedProcess Branch + OBI branch derived + definition blessed by Allyson, Bjoern, Jay & Randi + non-specific labeling + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell fixation + http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus + + a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time + should include capturing what qualities are being preserved + PERSON:Bjoern Peters + OBI branch derived + we could generalize this for other input materials + cell fixation + + + + + + + + + + + + + + + excision + Cutting out the portion of a gel which contains a DNA fragment + + the use physical means to remove a portion of a substance from the rest + Alan Ruttenberg, Kevin Clancy + www.crohnsresource.com/glossary.jsp (via google define:resection) + excision + + + + + + + + + + non specific enzymatic cleavage + The use of agarase to digest an agar gel + + an enzymatic cleavage that uses an enzyme without a strong affinity for specific cleavage sites in the input material + PERSON:Kevin Clancy + OBI branch derived + non specific enzymatic cleavage + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + maintaining cell culture + When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture + + a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing + PlanAndPlannedProcess Branch + OBI branch derived + maintaining cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + artificially induced cell membrane lysis + http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent. + + a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate + ---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined. + PlanAndPlannedProcess Branch + OBI branch derived + artificially induced cell membrane lysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + artificially induced reverse transcription + 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. + 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 + artificially induced reverse transcription + + + + + + + + + + + + + + + isolation of cell culture supernatant + Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube. + + a protocol which results in the separation of supernatant material from a cell culture + This does not apply to the case where the cells are lysed + PlanAndPlannedProcess Branch + OBI branch derived + isolation of cell culture supernatant + + + + + + + + + + + + + + + experimental disease induction + the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome. + + a protocol application to induce a specific disease in an organism + PlanAndPlannedProcess Branch + OBI branch derived + could be defined class + experimental disease induction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + artificially induced DNA repair + the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands + + a protocol application to repair damaged DNA molecules + PlanAndPlannedProcess Branch + OBI branch derived + ---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi + artificially induced DNA repair + + + + + + + + + + + + + + + + + + + + + + + + + + + cell permeabilization + Electroporation of HeLa cells to allow transfection with pUC19. + + A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application + need to add output cell has_quality permeable + PERSON:Bjoern Peters + OBI branch derived + definition blessed by Jay, Alan, Randi + cell permeabilization + + + + + + + + + + + + + + + precipitation + The use of ethanol to precipitate DNA molecules from a solution containing DNA + + a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate) + PERSON:Kevin Clancy + OBI branch derived + precipitation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'establishing cell culture' + + a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). + PERSON:Matthew Brush + PERSON:Matthew Brush + A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. + establishing cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + cell culture splitting + The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. + + 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 + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + addition of molecular label + The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. + + 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 + OBI developer call, 3-12-12 + addition of molecular label + + + + + + + + + + + + + + + artificially induced methylation + the use of enzymes to add methyl groups to DNA molecules + + A planned process of adding methyl groups to polymers + PERSON:Kevin Clancy + OBI branch derived + artificially induced methylation + + + + + + + + + + + + + + + + + + + + + + + + + + + synthesis + making cDNA from nucleotides using RNA as a template + + the construction of a biomaterial from simpler biomaterials + This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription + PERSON:Kevin Clancy + synthesize + OBI branch derived + synthesis + + + + + + + + + + + + + + + concentrate + Evaporation of the solution containing DNA to increase the concentration of the DNA molecules + + a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material + PERSON:Kevin Clancy + OBI branch derived + concentrate + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + recombinant plasmid cloning + The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35. + + the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial + PERSON:Kevin Clancy + OBI branch derived + recombinant plasmid cloning + + + + + + + + + + + + + + + + + + + + + genetic transformation + The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 + + the introduction. alteration or integration of genetic material into a cell or organism + PERSON:Kevin Clancy + genetic modification + OBI branch derived + genetic transformation + + + + + + + + + + + + + + + + lavage + the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present + + A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid + This is not washing, in which case the material of interest is not the resulting fluid + PlanAndPlannedProcess Branch + OBI branch derived + lavage + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + preparative chromatography + The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides. + + the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity + PERSON:Kevin Clancy; Bjoern Peters + OBI branch derived + preparative chromatography + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + PERSON:Kevin Clancy + OBI branch derived + vector mediated amplification + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DNA polymerase amplification + The use of taq polymerase to amplify a DNA fragment during a PCR. + + 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 + OBI branch derived + DNA polymerase amplification + + + + + + + + + specific enzymatic cleavage + The use of a protease to digest a protein into peptides + + an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material + PERSON:Kevin Clancy + OBI branch derived + specific enzymatic cleavage + + + + + + + + + + + + + + + gradient separation + the use of a sucrose gradient to isolate mitochondria + + a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities + PERSON:Kevin Clancy + OBI branch derived + gradient separation + + + + + + + + + + + + + + + dialysis + the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage + + a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition + PERSON:Kevin Clancy + OBI branch derived + dialysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + electrophoresis + Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change. + + a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge + PERSON:Kevin Clancy + OBI branch derived + Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers. + electrophoresis + + + + + + + + + + + + + + + selection by survival + The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected + + the use of environmental conditions to select for the organism or cells that have a certain trait + PERSON:Kevin Clancy + OBI branch derived + selection by survival + + + + + + + + + + + + + + + DNA cleavage, restriction analysis + the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components + + A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence + PERSON:Kevin Clancy + restriction enzyme assay + DNA restriction enzyme digestion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + protease cleavage + the use of trypsin to cleave pepsin into peptide fragments + + protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). + enzymatic digestion + PlanAndPlannedProcess Branch + OBI branch derived + protease cleavage + + + + + + + + + enzymatic DNA replication + the use of enzymes to duplicate DNA molecules + + the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial + PERSON:Kevin Clancy + OBI branch derived + enzymatic DNA replication + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + enzymatic amplification + the use of a polymerase chain reaction to amplify a fragment of DNA + + the use of enzymes to increase the number of molecules of a biomaterial + PERSON:Kevin Clancy + OBI branch derived + enzymatic amplification + + + + + + + + + + + + + + + DNA transduction + The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein + + a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism + PERSON:Kevin Clancy + OBI branch derived + DNA transduction + + + + + + + + + + + + + + + + + + + + + + + + + DNA transfection + The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest + + a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell + PERSON:Kevin Clancy + OBI branch derived + DNA transfection + + + + + + + + + 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. + + 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 + PlanAndPlannedProcess Branch + OBI branch derived + vector mediated expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + recombinant vector cloning + + 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 + OBI branch derived + recombinant vector cloning + + + + + + + + + obsolete_defined processes + + Place holder class, see editor note + PlanAndPlannedProcess Branch + OBI branch derived + + obsolete_defined processes + true + + + + + + + + + specific labeling + The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells + + a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material + PlanAndPlannedProcess Branch + OBI branch derived + definition blessed by Allyson, Bjoern, Jay & Randi + specific labeling + + + + + + + + + + + + + + + RNA extraction + + A RNA extraction is a nucleic acid extraction where the desired output material is RNA + PlanAndPlannedProcess Branch + OBI branch derived + requested by Helen Parkinson for MO + RNA extraction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nucleic acid extraction + Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. + + a material separation to recover the nucleic acid fraction of an input material + PlanAndPlannedProcess Branch + OBI branch derived + requested by Helen Parkinson for MO. Could be defined class + nucleic acid extraction + + + + + + + + + + + + + + + + + + + + + cell culture supernatant + solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. +Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615 + + Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell. + PERSON: Bjoern Peters + GROUP: IEDB + cell culture supernatant + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell pellet + Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214 + + 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 + GROUP: CEBS + GROUP: OBI Biomaterial Branch + cell pellet + + + + + + + + + + + + + + + + + + + + + phage display library + PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] + + a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + display library + WEB: http://www.immuneepitope.org/home.do + PRS: 22022008. class moved under population, +modification of definition and replacement of biomaterials in previous definition with 'material' +addition of has_role restriction + phage display library + + + + + + + + + + + + + + + + + + + + + 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 + + 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 + GROUP: PSI + cell lysate + + + + + + + + + + + + + + + + + + + + + peptide construct + Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin + +A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617 + + a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion + PERSON: Bjoern Peters + IEDB + peptide construct + + + + + + + + + + + + + + + transgenic organism + HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein +Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162 + + 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 + GROUP:IEDB + transgenic organism + + + + + + + + + + + + + + + + + + + + + + + whole mount tissue + + 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 + whole mount sample + GROUP: OBI + PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity + PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application + whole mount tissue + + + + + + + + + assay bead + Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. + + A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. + DS: Probably better modeled as a role. + OBI + bead + assay bead + + + + + + + + + + + + + + + epitope + + a material entity bearing the epitope role + IEDB + IEDB + epitope + + + + + + + + + obsolete_occurrence of disease + + An occurrence of disease is a process involving pathologic changes within an organism + IEDB + IEDB + + obsolete_occurrence of disease + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + host exposure to infectious agent + + a process in which an infectious agent comes into physical contact with a host organism. + IEDB + IEDB + host exposure to infectious agent + + + + + + + + + + + + + + + + + + + + + + + + + administration in vivo with infectious agent + + is an administration of an infectious agent to a host organism + IEDB + IEDB + administration in vivo with infectious agent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + occurrence of infectious disease + + Is an occurrence of a disease caused by an infection + IEDB + IEDB + occurrence of infectious disease + + + + + + + + + + + + + + + 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 + IEDB + disposition to cause an 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 + IEDB + allergic reaction + + + + + + + + + + + + + + + + + + + + + occurrence of allergy + + The process of an allergic disease occurring in an organism. + IEDB + IEDB + occurrence of allergy + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-2 production by T cells + + An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-2 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + epitope binding by adaptive immune receptor + + + + + + + + + + + + + + + Immunization in vivo + + Process of administering an object playing the role of immunogen to a living organism + IEDB + IEDB + Immunization in vivo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + adaptive immune effector function + + + + + + + + + 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 + IEDB + IEDB + living with infected household contact + + + + + + + + + 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 + IEDB + IEDB + living in endemic area + + + + + + + + + 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 + IEDB + IEDB + pathogen release in laboratory accident + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Immunization in vitro + + Process of administering an object playing the role of immunogen to a cell culture + IEDB + IEDB + Immunization in vitro + + + + + + + + + + + + + + + + + + + + + infection process + + the detrimental process in which an infectious agent colonizes or replicates in a host environment + IEDB + IEDB + infection process + + + + + + + + + + + + + + + + + + adaptive immune receptor + + is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. + IEDB + IEDB + adaptive immune receptor + + + + + + + + + + + + + + + immunogen + + a material entity bearing the immunogen role + IEDB + IEDB + immunogen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + environmental exposure to infectious agent + + + + + + + + + + + + + + + + + + + + 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. + IEDB + IEDB + host of immune response + + + + + + + + + 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. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl5008.html + 293-T 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)). + IEDB + IEDB + C1R cell line + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + experimental infection of cell culture + + + + + + + + + EL-4 cell line + + A cell line derived from mouse (C57BL/6N) lymphoma cells. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl1160.html + EL-4 cell line + + + + + + + + + HeLa cell culture + + A cell line derived from human cervical cancer cells. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl1597.html + HeLa cell line + + + + + + + + + JAWS II cell line + + 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 + JAWS II cell line + + + + + + + + + + + + + + + antigen + + is a material entity that has the antigen role + IEDB + IEDB + antigen + + + + + + + + + Jurkat cell line + + A cell line derived from human T cells. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl5296.html + Jurkat cell line + + + + + + + + + JY cell line + + The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) + IEDB + IEDB + JY cell line + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring binding of a T cell epitope:MHC:TCR complex + + An immune epitope assay that detects T cell epitope recognition. + IEDB + IEDB + T cell binding|any method + assay measuring binding of a T cell epitope:MHC:TCR complex + + + + + + + + + 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. + IEDB + IEDB + RMA cell line + + + + + + + + + T2 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 + T2 cell line + + + + + + + + + infectious disease + + is a disease caused by an infectious agent + IEDB + IEDB + infectious disease + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + IEDB + IEDB + lymph node cell specimen + + + + + + + + + + + + + + + + + + + + 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. + 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. + IEDB + adherent cell culture sample + IEDB + cultured adherent cell populaiton + + + + + + + + + + + + + + + + + + + + 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). + IEDB + PBMC cell culture sample + IEDB + cultured PBMC cell population + + + + + + + + + + + + + + + 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 + IEDB + disposition to be bound by an adaptive immune receptor + + + + + + + + + organ harvesting + + The process of removing an organ from its source organism + IEDB + IEDB + organ harvesting + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured CD3+ T cell population + + A T cell population characterized by expressing the CD3 molecule on its surface. + IEDB + CD3+ T cell culture sample + IEDB + cultured CD3+ T cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured CD3- T cell population + + A T cell population characterized by not expressing the CD3 molecule on its surface. + IEDB + CD3- T cell culture sample + IEDB + cultured CD3- T cell population + + + + + + + + + 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 + IEDB + allergy + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured CD4- T cell population + + A T cell population characterized by not expressing the CD4 molecule on its surface. + IEDB + CD4- T cell culture sample + IEDB + cultured CD4- T cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured CD8- T cell population + + A T cell population characterized by not expressing the CD8 molecule on its surface. + IEDB + CD8- T cell culture sample + IEDB + cultured 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. + IEDB + CD4-/CD8- T cell culture sample + IEDB + cultured CD4-/CD8- T cell population + + + + + + + + + cancer + + A disease characterized by abnormal and uncontrolled cell division + IEDB + IEDB + cancer + + + + + + + + + autoimmune disease + + Is a disease characterized by an immune response of an organism against parts of itself + IEDB + IEDB + autoimmune disease + + + + + + + + + obsolete_disease + + placeholder to be imported from disease ontology + IEDB + IEDB + + + obsolete_disease + true + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + epitope specific IL-2 release by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + MHC:epitope complex binding to TCR + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interferon-gamma production by T cells + + An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ELISPOT + ELISPOT assay measuring epitope specific interferon-gamma production by T cells + + + + + + + + + exposure resulting in 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 + + + + + + + + + immunogen role + + any entity capable of eliciting an immune response when introduced to components of the immune system + IEDB + IEDB + immunogen 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. + IEDB + IEDB + host of immune response role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + effector T cell 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. + antigen presentation function + + + + + + + + + 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 + IEDB + restricting MHC role + + + + + + + + + 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 + IEDB + Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. + donor + + + + + + + + + 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. + IEDB + IEDB + immune epitope carrier 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 + IEDB + adjuvant role + + + + + + + + + + + + + + + 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 + IEDB + disposition to infect an organism + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + immunization + + + + + + + + + + + + + + + blood harvesting + + A material separation where blood is taken from an organism. + IEDB + IEDB + blood harvesting + + + + + + + + + L cell line + + A cell line derived from mouse fibroblasts. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl3075.html + L cell line + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + antigen presenting cell culture sample + IEDB + cultured antigen presenting cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured effector T cell population + A culture of cytotoxic CD8+ T cells. + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + IEDB + environmental proximity to infectious agent + + + + + + + + + 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 + IEDB + IEDB + contact to pathogen carrying biological vector + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + IEDB + IEDB + splenocyte specimen + + + + + + + + + P815 cell line + + A cell line derived from mouse mastocytoma. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl5244.html + P815 cell line + + + + + + + + + + + + + + + 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 + IEDB + assay antigen role + + + + + + + + + pathologic process + + abnormal, harmful processes caused by or associated with a disease + IEDB + IEDB + pathologic process + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex + + A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|binding assay + assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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|binding assay + assay measuring binding of a MHC:ligand complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + assay measuring binding of a B cell epitope:antibody complex + + An immune epitope assay that detects B cell epitope recognition. + IEDB + IEDB + antibody binding|any method + assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + immune epitope assay + + An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event + IEDB + IEDB + immune epitope assay + immune epitope assay + + + + + + + + + + + + + + + + + + + + biological activity assay measuring epitope specific cytokine production by T cells + + A T cell epitope dependent biological activity assay that detects cytokine production. + IEDB + IEDB + cytokine release|biological activity + biological activity assay measuring epitope specific cytokine production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + biological activity 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + biological activity 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 + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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. + IEDB + IEDB + cytotoxicity|51 chromium + 51 chromium assay measuring epitope specific T cell killing + + + + + + + + + + + + + + + + + + + + ELISA measuring epitope specific interferon-gamma production by T cells + + An assay of epitope specific interferon-gamma production by T cells that uses an ELISA. + 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 interleukin-2 production by T cells + + An assay of epitope specific interleukin-2 production by T cells that uses an ELISA. + 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-4 production by T cells + + An assay of epitope specific interleukin-4 production by T cells that uses an ELISA. + 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-5 production by T cells + + An assay of epitope specific interleukin-5 production by T cells that uses an ELISA. + 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 tumor necrosis factor production by T cells + + A T cell epitope specific tumor necrosis factor production assay that uses an ELISA. + 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 interleukin-10 production by T cells + + An assay of epitope specific interleukin-10 production by T cells that uses an ELISA. + 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 granulocyte macrophage colony-stimulating factor production by T cells + + An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA. + 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 interleukin-6 production by T cells + + An assay of epitope specific interleukin-6 production by T cells that uses an ELISA. + 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-13 production by T cells + + An assay of epitope specific interleukin-13 production by T cells that uses an ELISA. + 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-12 production by T cells + + An assay of epitope specific interleukin-12 production by T cells that uses an ELISA. + 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-1 beta production by T cells + + An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA. + 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-17 production by T cells + + An assay of epitope specific interleukin-17 production by T cells that uses an ELISA. + 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 assay of epitope specific interleukin-18 production by T cells that uses an ELISA. + 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 assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay. + 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 + + A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay. + IEDB + IEDB + TNFa release|ELISPOT + ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells + + + + + + + + + + + + + + + + + + + + ELISPOT assay measuring epitope specific interleukin-10 production by T cells + + An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay. + 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 assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay. + 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 + + An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay. + 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 + + An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay. + 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 production by T cells + + A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay. + 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 interleukin-4 production by T cells + + An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay. + 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 + + An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay. + 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 + + An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay. + 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 T cell epitope qualitative binding assay that uses an MHC multimer staining assay. + 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. + IEDB + IEDB + proliferation|BrdU + BrdU assay measuring epitope specific proliferation of T cells + + + + + + + + + + + + + + + + + + + + epitope specific T cell proliferation + + A biological process where T cells proliferate resulting from the recognition of a T cell epitope. + IEDB + IEDB + epitope specific T cell proliferation + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + epitope specific GM-CSF 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 + IEDB + epitope specific IFN-g 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 + IEDB + epitope specific IL-10 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 + IEDB + epitope specific IL-12 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 + IEDB + epitope specific IL-13 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 + IEDB + epitope specific IL-17 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 + IEDB + epitope specific IL-18 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 + IEDB + epitope specific IL-1b 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 + IEDB + epitope specific IL-4 release by T cells + + + + + + + + + + + + + + + + + + + + allergen + Birch pollen is an allergen + + A material entity bearing the disposition to cause an allergic reaction + IEDB + IEDB + allergen + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + epitope specific IL-5 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 + IEDB + epitope specific IL-6 release 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 + IEDB + epitope specific killing 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 + IEDB + epitope specific TNF release by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + FFPE specimen + 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 + + + FFPE specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + uterine cervix specimen + + A specimen that is derived from some uterine cervix + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + uterine cervix specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + urethra specimen + + A specimen that is derived from some urethra + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + urethra specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + cervical mucus specimen + + A specimen that is derived from some cervical mucus + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + cervical mucus specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + throat specimen + + A specimen that is derived from some throat + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + throat specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + eye specimen + + A specimen that is derived from some eye + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + eye specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + respiratory system specimen + + A specimen that is derived from some respiratory system + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + respiratory system specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + upper respiratory tract specimen + + A specimen that is derived from some upper respiratory tract + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + upper respiratory tract specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + nasopharynx specimen + + A specimen that is derived from some nasopharynx + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + nasopharynx specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + semen specimen + + A specimen that is derived from some semen + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + semen specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + bodily fluid specimen + + A specimen that is derived from some bodily fluid + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + bodily fluid specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + chorionic villus specimen + + A specimen that is derived from some chorionic villus + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + chorionic villus specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + meconium specimen + + A specimen that is derived from some meconium + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + meconium specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + umbilical cord blood specimen + + A specimen that is derived from some umbilical cord blood + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + umbilical cord blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + arterial blood specimen + + A specimen that is derived from some arterial blood + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + arterial blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + venous blood specimen + + A specimen that is derived from some venous blood + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + venous blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + capillary blood specimen + + A specimen that is derived from some capillary blood + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + capillary blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + erythrocyte specimen + + A specimen that is derived from some erythrocytes + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + erythrocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + reticulocyte specimen + + A specimen that is derived from some reticulocytes + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + reticulocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + leukocyte specimen + + A specimen that is derived from some leukocytes + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + leukocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + + - + - + - - + + - + - + - - + + @@ -88097,683 +114772,764 @@ Possible ecological risks of transgenic organism release when transgenes affect - - - host exposure to infectious agent - - a process in which an infectious agent comes into physical contact with a host organism. - IEDB - IEDB - host exposure to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - administration in vivo with infectious agent - - is an administration of an infectious agent to a host organism - IEDB - IEDB - administration in vivo with infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - occurrence of infectious disease - - Is an occurrence of a disease caused by an infection - IEDB - IEDB - occurrence of infectious disease + 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 - + - - + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - 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 - IEDB - disposition to cause an allergic reaction - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - allergic reaction + ionized venous blood calcium assay - an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen) - IEDB - IEDB - allergic reaction + 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 - + - - - - - - - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - occurrence of allergy - - The process of an allergic disease occurring in an organism. - IEDB - IEDB - occurrence of allergy - - - - - - - - + - - - + + + + + + + + + + + + + + + + - - - ELISPOT assay measuring epitope specific interleukin-2 production by T cells + + venous blood hemoglobin assay - An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-2 production by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - IEDB - epitope binding by adaptive immune receptor + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Immunization in vivo - - Process of administering an object playing the role of immunogen to a living organism - IEDB - IEDB - Immunization in vivo - - - - - - - - - + - - - - - - - + + + + - - - - - - - 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 - IEDB - adaptive immune effector function - - - - - - - - - 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 - IEDB - IEDB - living with infected household contact - - - - - - - - - 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 - IEDB - IEDB - living in endemic area - - - - - - - - - pathogen release in laboratory accident + CBC with manual differential venous blood megakaryocyte count assay - 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 + 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 - + - - - - - - - - + + - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + - Immunization in vitro - - Process of administering an object playing the role of immunogen to a cell culture - IEDB - IEDB - Immunization in vitro + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + - infection process + intraoperative venous blood PTH assay - the detrimental process in which an infectious agent colonizes or replicates in a host environment - IEDB - IEDB - infection process + 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 - + - - + + + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - adaptive immune receptor - - is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. - IEDB - IEDB - adaptive immune receptor - - - - - - - - - - - - - - - immunogen + + + + + + + + + + + + + + + + + + + + + + + + + + venous blood parathyroid hormone assay - a material entity bearing the immunogen role - IEDB - IEDB - immunogen + 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 - + - - + + + - - + - - - - - - - - - - - - - + + + + + + + + + + + + + + + - + + + + + + + - - + + + + + + + + + + + + + + + + - - - 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 - IEDB - environmental exposure to infectious agent + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - 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. + + + + + + + + + + + + + + + + + + + + + + + + + + bodily fluid glucose assay - 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. - IEDB - IEDB - host of immune response - - - - - - - - - 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. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl5008.html - 293-T 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)). - IEDB - IEDB - C1R cell line + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + + + - 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 - IEDB - experimental infection of cell culture - - - - - - - - - EL-4 cell line - - A cell line derived from mouse (C57BL/6N) lymphoma cells. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl1160.html - EL-4 cell line - - - - - - - - - HeLa cell culture - - A cell line derived from human cervical cancer cells. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl1597.html - HeLa cell line - - - - - - - - - JAWS II cell line - - 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 - JAWS II cell line + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + - - - antigen - - is a material entity that has the antigen role - IEDB - IEDB - antigen - - - - - - - - - Jurkat cell line - - A cell line derived from human T cells. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl5296.html - Jurkat cell line - - - - - - - - - JY cell line - - The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) - IEDB - IEDB - JY cell line + + 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 - + - - + + + - - + - + - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -88781,199 +115537,578 @@ Possible ecological risks of transgenic organism release when transgenes affect - - - assay measuring binding of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + manual differential bodily fluid mesothelial cell count assay - An immune epitope assay that detects T cell epitope recognition. - IEDB - IEDB - T cell binding|any method - assay measuring binding of a T cell epitope:MHC:TCR complex + 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 - + - - - RMA cell line + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + manual differential bodily fluid monocyte count assay - 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 + 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 - + - - - T2 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 - T2 cell line + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - infectious disease - - is a disease caused by an infectious agent - IEDB - IEDB - infectious disease + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + + + - 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. - IEDB - IEDB - lymph node cell specimen + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - 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. - 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. - IEDB - adherent cell culture sample - IEDB - cultured adherent cell populaiton + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - 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). - IEDB - PBMC cell culture sample - IEDB - cultured PBMC cell population + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - 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 - IEDB - disposition to be bound by an adaptive immune receptor + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - organ harvesting - - The process of removing an organ from its source organism - IEDB - IEDB - organ harvesting + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + + - - + - + - - + + + + + + + + + + + + + + + + @@ -88981,745 +116116,849 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - cultured CD3+ T cell population - - A T cell population characterized by expressing the CD3 molecule on its surface. - IEDB - CD3+ T cell culture sample - IEDB - cultured CD3+ T cell population - - - - - - - - + + - - + - - - - - - - - - + + + + + + + + + - - - cultured CD3- T cell population - - A T cell population characterized by not expressing the CD3 molecule on its surface. - IEDB - CD3- T cell culture sample - IEDB - cultured CD3- T cell population - - - - - - - - - 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 - IEDB - allergy + + 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 - + - - + + + - - + - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - - cultured CD4- T cell population - - A T cell population characterized by not expressing the CD4 molecule on its surface. - IEDB - CD4- T cell culture sample - IEDB - cultured CD4- T cell population - - - - - - - - + + - - + - - - - - - - - - + + + + + + + + + - - - cultured CD8- T cell population - - A T cell population characterized by not expressing the CD8 molecule on its surface. - IEDB - CD8- T cell culture sample - IEDB - cultured CD8- T cell population + + 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 - + - - + + + - - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - - - cultured CD4-/CD8- T cell population - - 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 - cultured CD4-/CD8- T cell population - - - - - - - - - cancer - - A disease characterized by abnormal and uncontrolled cell division - IEDB - IEDB - cancer - - - - - - - - - autoimmune disease - - Is a disease characterized by an immune response of an organism against parts of itself - IEDB - IEDB - autoimmune disease - - - - - - - - - obsolete_disease - - placeholder to be imported from disease ontology - IEDB - IEDB - - - obsolete_disease - true - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - - - 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 - IEDB - epitope specific IL-2 release by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MHC:epitope complex binding to TCR + liver function venous blood human alkaline phosphatase assay - 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 - IEDB - MHC:epitope complex binding to TCR + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISPOT assay measuring epitope specific interferon-gamma production by T cells - - An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ELISPOT - ELISPOT assay measuring epitope specific interferon-gamma production by T cells - - - - - - - - - exposure resulting in 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 - - - - - - - - - immunogen role - - any entity capable of eliciting an immune response when introduced to components of the immune system - IEDB - IEDB - immunogen 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. - IEDB - IEDB - host of immune response role + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - + + + + + + + - 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 - IEDB - effector T cell function + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + + + - antigen presentation function + venous blood reticulocyte count assay - 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. - antigen presentation function - - - - - - - - - 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 - IEDB - restricting MHC role + 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 - + - - - donor - A T cell line from a PPD(+) donor. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bodily fluid cholesterol assay - 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 - IEDB - Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. - donor - - - - - - - - - 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. - IEDB - IEDB - immune epitope carrier role + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + - 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 - IEDB - adjuvant role + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - 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 - IEDB - disposition to infect an organism + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + - + - - - - - - + - - + + + + + + - - - 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 - IEDB - immunization + + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - blood harvesting - - A material separation where blood is taken from an organism. - IEDB - IEDB - blood harvesting - - - - - - - - - L cell line - - A cell line derived from mouse fibroblasts. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl3075.html - L cell line + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + - + - - + + + + + + - - - cultured antigen presenting cell population - A culture of PBMCs. A culture of Hela cells. + + bodily fluid triglyceride assay - a cell culture including cells that have an antigen presentation function - antigen presenting cell culture sample - IEDB - cultured antigen presenting cell population + 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 - + - - + + + - - + - + - - + + + + + + + + + + + + + + + + @@ -89727,297 +116966,206 @@ 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. - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - IEDB - environmental proximity to infectious agent - - - - - - - - - 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 - IEDB - IEDB - contact to pathogen carrying biological vector - - - - - - - - - + - + - - - - - - - - - + + + + - splenocyte specimen + hemoglobin and hematocrit venous blood hematocrit assay - 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 - - - - - - - - - P815 cell line - - A cell line derived from mouse mastocytoma. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl5244.html - P815 cell line + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - 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 - IEDB - assay antigen role - - - - - - - - - pathologic process - - abnormal, harmful processes caused by or associated with a disease - IEDB - IEDB - pathologic process - - - - - - - - + - - + - + - - + + + + + + - - - assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex + + hemoglobin and hematocrit venous blood hemoglobin assay - A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|binding assay - assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex + 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 - + - - + + + + - + + + + + + + + + + + + + + - + - - + + + + + + + + - + - + - - - - - - - - - - - - + + + + + + - - - assay measuring MHC ligand processing and presentation + + venous blood ionized calcium assay - 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 + 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 - + - - + + + - - + - + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -90025,45 +117173,59 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - assay measuring binding of a MHC:ligand complex + + + + + + + + + + + + + venous blood temperature assay - A MHC ligand assay that detects the binding of a ligand to an MHC molecule. - IEDB - IEDB - MHC binding|binding assay - assay measuring binding of a MHC:ligand complex + 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 - + - - + + + - - + - + - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -90071,125 +117233,145 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - assay measuring binding of a B cell epitope:antibody complex - - An immune epitope assay that detects B cell epitope recognition. - IEDB - IEDB - antibody binding|any method - assay measuring binding of a B cell epitope:antibody complex - - - - - - - - - immune epitope assay - - An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event - IEDB - IEDB - immune epitope assay - immune epitope assay - - - - - - - - + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + - biological activity assay measuring epitope specific cytokine production by T cells + venous blood bicarbonate assay - A T cell epitope dependent biological activity assay that detects cytokine production. - IEDB - IEDB - cytokine release|biological activity - biological activity assay measuring epitope specific cytokine production by T cells + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - + - + - - + + + + + + - - - biological activity assay measuring epitope specific T cell killing + + venous blood oxygen assay - 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 + 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 - + - - + + + - - - + + + + + + + + + + + + - + - + - - + + @@ -90197,1165 +117379,1815 @@ 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 + + + + + + + + + + + + + venous blood osmolality assay - 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 - - - - - - - - - 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 + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - 51 chromium assay measuring epitope specific T cell killing + + + + + + + + + + + + + liver fibrosis (chronic viral hepatitis) venous blood platelet count assay - 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 + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interferon-gamma production by T cells - - An assay of epitope specific interferon-gamma production by T cells that uses an ELISA. - 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 interleukin-2 production by T cells + + venous blood T3 assay - An assay of epitope specific interleukin-2 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ELISA - ELISA measuring epitope specific interleukin-2 production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interleukin-4 production by T cells + + + + + + + + + + + + + CBC with manual differential venous blood neutrophil count assay - An assay of epitope specific interleukin-4 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ELISA - ELISA measuring epitope specific interleukin-4 production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interleukin-5 production by T cells - - An assay of epitope specific interleukin-5 production by T cells that uses an ELISA. - 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 tumor necrosis factor production by T cells + + creatinine clearance urine creatinine assay - A T cell epitope specific tumor necrosis factor production assay that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|ELISA - ELISA measuring epitope specific tumor necrosis factor production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interleukin-10 production by T cells - - An assay of epitope specific interleukin-10 production by T cells that uses an ELISA. - 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 granulocyte macrophage colony-stimulating factor production by T cells + + venous blood beta hydroxybutryic acid assay - An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA. - 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 + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interleukin-6 production by T cells + + + + + + + + + + + + + venous blood megakaryocyte count assay - An assay of epitope specific interleukin-6 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|ELISA - ELISA measuring epitope specific interleukin-6 production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interleukin-13 production by T cells + + + + + + + + + + + + + venous blood nucleated RBC count assay - An assay of epitope specific interleukin-13 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISA - ELISA measuring epitope specific interleukin-13 production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interleukin-12 production by T cells + + + + + + + + + + + + + venous blood WBC count assay - An assay of epitope specific interleukin-12 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|ELISA - ELISA measuring epitope specific interleukin-12 production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interleukin-1 beta production by T cells + + + + + + + + + + + + + automated count venous blood reticulocyte count assay - An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|ELISA - ELISA measuring epitope specific interleukin-1 beta production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISA measuring epitope specific interleukin-17 production by T cells - - An assay of epitope specific interleukin-17 production by T cells that uses an ELISA. - 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 + + total venous blood homocysteine assay - An assay of epitope specific interleukin-18 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ELISA - ELISA measuring epitope specific interleukin-18 production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISPOT assay measuring epitope specific interleukin-4 production by T cells - - An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay. - 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 + + venous blood Ceruloplasmin assay - A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay. - IEDB - IEDB - TNFa release|ELISPOT - ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - ELISPOT assay measuring epitope specific interleukin-10 production by T cells - - An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay. - 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 + + GEM4 arterial blood bicarbonate assay - An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-13 production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells + + + + + + + + + + + + + GEM4 arterial blood lactic acid assay - An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ICS - intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells - - An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay. - 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 production by T cells + + GEM4 arterial blood hemoglobin assay - A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay. - 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 + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells + + GEM4 arterial blood sodium assay - An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay. - 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 + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells - - An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay. - 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 + + GEM4 arterial blood potassium assay - An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay. - 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 + 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 - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + GEM4 arterial blood temperature assay - A T cell epitope qualitative binding assay that uses an MHC multimer staining assay. - 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 + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - 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 + + GEM4 arterial blood glucose assay - 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 + 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 - + - - + + + - - - + + + + + + + + + + + + - - - - - epitope specific T cell proliferation - - A biological process where T cells proliferate resulting from the recognition of a T cell epitope. - IEDB - IEDB - epitope specific T cell proliferation - - - - - - - - - - - - - + + + + + + + + + + + + - - - - 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 - IEDB - epitope specific GM-CSF release by T cells - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - - - epitope specific IFN-g release by T cells + + GEM4 arterial blood oxygen assay - A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope. - IEDB - IEDB - epitope specific IFN-g release by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + - - - - - - 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 - IEDB - epitope specific IL-10 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 - IEDB - epitope specific IL-12 release by T cells + + + + + + + + + + + + + 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 - + - - + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - 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 - IEDB - epitope specific IL-13 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 - IEDB - epitope specific IL-17 release by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - 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 - IEDB - epitope specific IL-18 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 - IEDB - epitope specific IL-1b release by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - 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 - IEDB - epitope specific IL-4 release by T cells + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - allergen - Birch pollen is an allergen - - A material entity bearing the disposition to cause an allergic reaction - IEDB - IEDB - allergen - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - - - 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 - IEDB - epitope specific IL-5 release by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - epitope specific IL-6 release by T cells + + + + + + + + + + + + + CBC with manual differential venous blood plasma cell count assay - A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope. - IEDB - IEDB - epitope specific IL-6 release by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - 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 - IEDB - epitope specific killing 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 - IEDB - epitope specific TNF release by T cells + + 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 - + - - + + + - - + - + - - + + + + + + + + + + + + + + + + @@ -91363,601 +119195,857 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - - 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 - - - - - - - - - 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 - - - - - - - - - FFPE specimen - 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 - - - FFPE specimen - - - - - - - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - - uterine cervix specimen + + blood gas arterial blood oxygen assay - A specimen that is derived from some uterine cervix - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - uterine cervix specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - urethra specimen - - A specimen that is derived from some urethra - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - urethra specimen - - - - - - - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - - cervical mucus specimen + + blood gas arterial blood bicarbonate assay - A specimen that is derived from some cervical mucus - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - cervical mucus specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - throat specimen - - A specimen that is derived from some throat - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - throat specimen - - - - - - - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - - eye specimen + + blood gas arterial blood carbon dioxide assay - A specimen that is derived from some eye - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - eye specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - respiratory system specimen - - A specimen that is derived from some respiratory system - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - respiratory system specimen - - - - - - - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - - upper respiratory tract specimen + + free/total venous blood PSA assay - A specimen that is derived from some upper respiratory tract - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - upper respiratory tract specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - nasopharynx specimen + + + + + + + + + + + + + cerebrospinal fluid lymphocyte count assay - A specimen that is derived from some nasopharynx - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - nasopharynx specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - semen specimen + + + + + + + + + + + + + cerebrospinal fluid segmented neutrophil count assay - A specimen that is derived from some semen - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - semen specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - bodily fluid specimen + + + + + + + + + + + + + cerebrospinal fluid mesothelial cell count assay - A specimen that is derived from some bodily fluid - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - bodily fluid specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - chorionic villus specimen + + + + + + + + + + + + + cerebrospinal fluid macrophage count assay - A specimen that is derived from some chorionic villus - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - chorionic villus specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - meconium specimen + + + + + + + + + + + + + cerebrospinal fluid basophil count assay - A specimen that is derived from some meconium - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - meconium specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - umbilical cord blood specimen + + + + + + + + + + + + + cerebrospinal fluid monocyte count assay - A specimen that is derived from some umbilical cord blood - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - umbilical cord blood specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - arterial blood specimen + + + + + + + + + + + + + cerebrospinal fluid eosinophil count assay - A specimen that is derived from some arterial blood - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - arterial blood specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - venous blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + venous blood beta-2-microglobulin assay - A specimen that is derived from some venous blood - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - venous blood specimen + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - capillary blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + lipid panel reflex direct venous blood low density lipoprotein assay - A specimen that is derived from some capillary blood - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - capillary blood specimen + 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 - + - - + + - - + - + - - + + + + + + + + + + + + + + + + @@ -91966,33 +120054,71 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - erythrocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + lipid panel reflex direct venous blood triglyceride assay - A specimen that is derived from some erythrocytes - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - erythrocyte specimen + 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 - + - - + + - - + - + - - + + + + + + + + + + + + + + + + @@ -92001,33 +120127,71 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - reticulocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + lipid panel reflex direct venous blood cholesterol assay - A specimen that is derived from some reticulocytes - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - reticulocyte specimen + 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 - + - - + + - - + - + - - + + + + + + + + + + + + + + + + @@ -92036,12 +120200,37 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - leukocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + lipid panel reflex direct venous blood high density lipoprotein assay - A specimen that is derived from some leukocytes - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - leukocyte specimen + 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 @@ -92173,7 +120362,7 @@ realizes some 'host of immune response role' treatment - A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate the signs and symptoms of a disorder or pathological process + 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 @@ -93045,6 +121234,18 @@ realizes some 'host of immune response role' + + + + + osmolality + A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent. + + osmolality + + + + @@ -93166,6 +121367,18 @@ realizes some 'host of immune response role' + + + + + prostate-specific antigen + A protein that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof. + + prostate-specific antigen + + + + @@ -93190,6 +121403,54 @@ realizes some 'host of immune response role' + + + + + 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 + + + + @@ -93202,6 +121463,18 @@ realizes some 'host of immune response role' + + + + + erythropoietin + A protein that is a translation product of the human EPO gene or a 1:1 ortholog thereof. + + erythropoietin + + + + @@ -93214,6 +121487,42 @@ realizes some 'host of immune response role' + + + + + 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 + + + + + + + + + parathyroid hormone + A protein that is a translation product of the human PTH gene or a 1:1 ortholog thereof. + + parathyroid hormone + + + + @@ -93226,6 +121535,30 @@ realizes some 'host of immune response role' + + + + + 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 + + + + @@ -93257,7 +121590,7 @@ realizes some 'host of immune response role' T cell receptor co-receptor CD8 - A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction. + 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 @@ -93324,6 +121657,101 @@ realizes some 'host of immune response role' + + + + + 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 + + + + @@ -94067,18 +122495,6 @@ realizes some 'host of immune response role' - - - - - nasal cavity - An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. - - nasal cavity - - - - @@ -94127,6 +122543,18 @@ realizes some 'host of immune response role' + + + + + nasal cavity mucosa + The mucous membrane that lines the nasal cavity[MP]. + + nasal cavity mucosa + + + + @@ -95313,19 +123741,8 @@ realizes some 'host of immune response role' - - - - - - - - - - - - - + + Affymetrix Affymetrix supplied microarray @@ -95338,13 +123755,7 @@ realizes some 'host of immune response role' - - - - - - - + Thermo Philippe Rocca-Serra @@ -95356,13 +123767,7 @@ realizes some 'host of immune response role' - - - - - - - + Waters Philippe Rocca-Serra @@ -95374,13 +123779,7 @@ realizes some 'host of immune response role' - - - - - - - + BIO-RAD Philippe Rocca-Serra @@ -95404,13 +123803,7 @@ realizes some 'host of immune response role' - - - - - - - + Ambion Philippe Rocca-Serra @@ -95422,13 +123815,7 @@ realizes some 'host of immune response role' - - - - - - - + Helicos Philippe Rocca-Serra @@ -95440,13 +123827,7 @@ realizes some 'host of immune response role' - - - - - - - + Roche Philippe Rocca-Serra @@ -95458,13 +123839,7 @@ realizes some 'host of immune response role' - - - - - - - + Illumina Philippe Rocca-Serra @@ -95537,13 +123912,7 @@ realizes some 'host of immune response role' - - - - - - - + Agilent Philippe Rocca-Serra @@ -95596,13 +123965,7 @@ realizes some 'host of immune response role' - - - - - - - + Li-Cor Philippe Rocca-Serra @@ -95614,13 +123977,7 @@ realizes some 'host of immune response role' - - - - - - - + Bruker Corporation Philippe Rocca-Serra @@ -95699,13 +124056,7 @@ realizes some 'host of immune response role' - - - - - - - + Applied Biosystems Philippe Rocca-Serra @@ -95745,13 +124096,7 @@ realizes some 'host of immune response role' - - - - - - - + Bruker Daltonics Philippe Rocca-Serra @@ -95817,13 +124162,7 @@ realizes some 'host of immune response role' - - - - - - - + Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 @@ -96004,13 +124343,7 @@ realizes some 'host of immune response role' - - - - - - - + U.S. Food and Drug Administration FDA @@ -96089,13 +124422,7 @@ realizes some 'host of immune response role' - - - - - - - + eBioscience A supplier of flow cytometry analyzers @@ -96109,13 +124436,7 @@ realizes some 'host of immune response role' - - - - - - - + Cytopeia A supplier of flow cytometry analyzers @@ -96129,13 +124450,7 @@ realizes some 'host of immune response role' - - - - - - - + Exalpha Biological A supplier of flow cytometry analyzers @@ -96149,13 +124464,7 @@ realizes some 'host of immune response role' - - - - - - - + Apogee Flow Systems A supplier of flow cytometry analyzers @@ -96169,13 +124478,7 @@ realizes some 'host of immune response role' - - - - - - - + Exbio Antibodies A supplier of flow cytometry analyzers @@ -96189,13 +124492,7 @@ realizes some 'host of immune response role' - - - - - - - + Becton Dickinson (BD Biosciences) A supplier of flow cytometry analyzers @@ -96209,13 +124506,7 @@ realizes some 'host of immune response role' - - - - - - - + Dako Cytomation A supplier of flow cytometry analyzers @@ -96229,13 +124520,7 @@ realizes some 'host of immune response role' - - - - - - - + Millipore A supplier of flow cytometry analyzers @@ -96249,13 +124534,7 @@ realizes some 'host of immune response role' - - - - - - - + Antigenix A supplier of flow cytometry analyzers @@ -96269,13 +124548,7 @@ realizes some 'host of immune response role' - - - - - - - + Partec A supplier of flow cytometry analyzers @@ -96289,13 +124562,7 @@ realizes some 'host of immune response role' - - - - - - - + Beckman Coulter A supplier of flow cytometry analyzers @@ -96309,13 +124576,7 @@ realizes some 'host of immune response role' - - - - - - - + Advanced Instruments Inc. (AI Companies) A supplier of flow cytometry analyzers @@ -96329,13 +124590,7 @@ realizes some 'host of immune response role' - - - - - - - + Miltenyi Biotec A supplier of flow cytometry analyzers @@ -96349,13 +124604,7 @@ realizes some 'host of immune response role' - - - - - - - + AES Chemunex A supplier of flow cytometry analyzers @@ -96369,13 +124618,7 @@ realizes some 'host of immune response role' - - - - - - - + Bentley Instruments A supplier of flow cytometry analyzers @@ -96389,13 +124632,7 @@ realizes some 'host of immune response role' - - - - - - - + Invitrogen A supplier of flow cytometry analyzers @@ -96409,13 +124646,7 @@ realizes some 'host of immune response role' - - - - - - - + Luminex A supplier of flow cytometry analyzers @@ -96429,13 +124660,7 @@ realizes some 'host of immune response role' - - - - - - - + CytoBuoy A supplier of flow cytometry analyzers @@ -96449,13 +124674,7 @@ realizes some 'host of immune response role' - - - - - - - + Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. @@ -96468,13 +124687,7 @@ 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. @@ -96487,13 +124700,7 @@ 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. @@ -98672,13 +126879,7 @@ 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. @@ -98692,13 +126893,7 @@ realizes some 'host of immune response role' - - - - - - - + BioGents An organization that manufactures mosquito traps and other mosquito control products. diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl index 3c4d19cc..2d8b5505 100644 --- a/views/NIAID-GSC-BRC.owl +++ b/views/NIAID-GSC-BRC.owl @@ -12,7 +12,7 @@ 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 @@ -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. - 2020-12-16 + 2021-04-06 @@ -118,13 +118,21 @@ + 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 @@ -160,7 +168,9 @@ 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 @@ -187,6 +197,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -1672,6 +1683,7 @@ 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 @@ -5991,6 +6003,36 @@ http://vivoweb.org/ontology/core#FundingOrganization + + + + + + + + + + + + + + + + + + + + + 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 + + + + diff --git a/views/obi-base.owl b/views/obi-base.owl index 1abde886..a5be30af 100644 --- a/views/obi-base.owl +++ b/views/obi-base.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. - 2020-08-26 + 2021-04-06 @@ -1603,12 +1603,54 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1621,12 +1663,54 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1647,24 +1731,84 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1677,6 +1821,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -1708,6 +1858,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -1752,6 +1908,24 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + @@ -1810,6 +1984,24 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + @@ -1823,6 +2015,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -1835,6 +2033,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + @@ -1922,12 +2132,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + @@ -2186,6 +2414,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -2198,6 +2432,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + @@ -2210,12 +2456,42 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2235,6 +2511,54 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2253,9 +2577,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - + @@ -2331,6 +2655,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -2373,6 +2703,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -2877,6 +3213,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -2943,6 +3285,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + + + + + + + + + + + + + + + + @@ -10812,7 +11178,9 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 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 @@ -14861,7 +15229,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - Measuring if a Hepatitis C virus (HCV) infected patient has an antibody response to HCV core protein by ELISA. + 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 @@ -18253,7 +18621,7 @@ stained with fecal material and is then placed in transport medium. - + @@ -25675,15 +26043,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -25926,15 +26289,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -26103,15 +26461,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -26136,15 +26489,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -26365,39 +26713,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -26454,15 +26773,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -26510,15 +26824,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -26543,15 +26852,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -26650,15 +26954,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -27012,15 +27311,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -27081,15 +27375,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -27329,39 +27618,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -27386,15 +27646,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -27521,15 +27776,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -27570,77 +27820,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -27652,14 +27832,8 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. + 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 @@ -27786,15 +27960,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -27885,15 +28054,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -28129,15 +28293,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -28214,15 +28373,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -28573,15 +28727,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -28966,25 +29115,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - + + + + @@ -29055,15 +29189,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -29222,15 +29351,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -29539,15 +29663,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -29595,25 +29714,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - + + + + @@ -29982,15 +30086,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -30356,15 +30455,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -30545,15 +30639,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -30601,15 +30690,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -30634,15 +30718,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -30936,15 +31015,10 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - + + + + @@ -31130,15 +31204,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - - + + + + @@ -31328,15 +31397,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - - + + + + @@ -31386,15 +31450,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - - + + + + @@ -31831,15 +31890,10 @@ pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) - - - - - - - - - + + + + @@ -32007,15 +32061,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -32124,15 +32173,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -32157,15 +32201,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -32190,15 +32229,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -32312,15 +32346,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -32368,15 +32397,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -32567,15 +32591,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -33303,44 +33322,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -33388,15 +33373,10 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - + + + + @@ -35817,15 +35797,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + @@ -36203,15 +36178,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + @@ -36649,15 +36619,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + @@ -36855,15 +36820,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + @@ -37770,25 +37730,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -37811,25 +37756,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -37852,25 +37782,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -37895,25 +37810,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -37938,25 +37838,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -37981,25 +37866,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -39581,25 +39451,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -39628,25 +39483,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -39671,25 +39511,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - - - - - - - - - - - + + + + @@ -39980,15 +39805,10 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - + + + + @@ -40011,20 +39831,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - + + + - - - - - - - + + - - + + @@ -40076,20 +39891,15 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - + + + - - - - - - - + + - - + + @@ -41765,15 +41575,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -41798,15 +41603,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -41831,15 +41631,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -41864,15 +41659,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -41897,15 +41687,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -41930,15 +41715,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -41963,15 +41743,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -41996,15 +41771,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -42696,15 +42466,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -42729,15 +42494,10 @@ is realized in a specimen collection process. - - - - - - - - - + + + + @@ -48250,7 +48010,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. - An assay that measures properties of cells. + An assay that counts and/or measures characteristics of cells. IEDB IEDB cytometry assay @@ -50701,20 +50461,15 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - + + + - - - - - - - + + - - + + @@ -50739,15 +50494,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - + + + + @@ -50772,15 +50522,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - + + + + @@ -50805,15 +50550,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - + + + + @@ -51172,15 +50912,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - + + + + @@ -52441,15 +52176,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -53087,7 +52817,7 @@ https://www.doi.org/ - An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepatitis C virus (HCV) antigens. + An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. Bjoern Peters Chris Stoeckert James Overton @@ -56236,15 +55966,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -58738,14 +58463,7 @@ https://www.doi.org/ - - - - - - - - + @@ -60928,25 +60646,10 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + @@ -60967,25 +60670,10 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - + + + + @@ -61012,15 +60700,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -61043,41 +60726,10 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -61098,41 +60750,10 @@ https://www.doi.org/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + @@ -61159,15 +60780,10 @@ https://www.doi.org/ - - - - - - - - - + + + + @@ -64067,4547 +63683,4656 @@ 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 - - - - - + - - + + + - + - + - - - - - - - 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 + + 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 - + - - - chimera - - An organism which contains cells or tissues with a different genotype - PERSON: Helen Parkinson - GROUP: OBI - chimera + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - + + - - - - - - - - - - - - - + - - + + + + + + + + + + + + - - - - 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 + + + + 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 - + - - - - - - + + + + - - - - - - - + - - + + + + + + + + + + + + - - - - - - - - - - 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 + + + + 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 - + - + - - - - - - + + + + + + + + + + + + + + + + + + + + + - - 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 + 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 - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - 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 + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. + + + 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. - 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 + 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 - + - - - - - - - - - - - - - specimen - Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. + + + 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 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 + 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 - + - - - - A material entity that represents generations of a primary culture. - PERSON: Susanna Sansone - GROUP: OBI Biomaterial Branch - - obsolete_cell line cell - true + + + 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 - + - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - - - - - - - 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. - - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - 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 + + + 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 - + - - - - - - - - - - - - - - - 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 + + + 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 - + - - - - 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 + + + 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 - + - - - - - - - - - glucose in solution - Glucose present in blood + + + personal protective clothing item - A scattered aggregate of glucose molecules in a liquid - PERSON: Jie Zheng - glucose molecules - glucose in solution + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. + + + laboratory coat - 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 + 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 - + - - - - - - - - - - - - - - - - - - - - - - - geometric mean calculation - 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). - geometric mean calculation + + + 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 - + - - - - - - - - - logistic-log curve fitting - Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve. + + + nitrile glove - A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). - Elisabetta Manduchi - James Malone - Melanie Courtot - Ryan Brinkman - ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 - logistic-log curve fitting + 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 - + - - - - - - - - - logit-log curve fitting - Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively. + + + transparent partition - A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. - The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model. - Elisabetta Manduchi - James Malone - Melanie Courtot - Ryan Brinkman - ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 - logit-log curve fitting + 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 - + - - - - - - - - - log-log curve fitting - Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. + + + footwear cover - A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. - Elisabetta Manduchi - James Malone - Melanie Courtot - Ryan Brinkman - ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 - log-log curve fitting + 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 - + - - - 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 - James Malone - TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction - feature extraction objective + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - biexponential transformation - This type of transformation is typically used in flow cytometry. + + + reusable footwear cover - A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - biexponential transformation + 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 - + - - - - - - - - - box-cox transformation + + + surgical N95 respirator - A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. - Ryan Brinkman - ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. - box-cox transformation + 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 - + - - - - - - - - - hyperlog transformation - This type of transformation is typically used in flow cytometry + + + protective coverall - A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42." - http://flowcyt.sourceforge.net/gating/latest.pdf - hyperlog transformation + 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 - + - - - loess scale group transformation one-channel - Loess scale group normalization applied to data from two one-channel expression microarray assays. + + + 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 loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. - Elisabetta Manduchi - OTHER: Editor's adjustment based on MGED Ontology term - loess scale group transformation one-channel + 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 - + - - - - - - - - - logical transformation - This type of transformation is typically used in flow cytometry. + + + + protective apron - A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - logical transformation + 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 - + - - - loess scale group transformation two-channel - Loess scale group normalization applied to data from a two-channel expression microarray assay. + + + medical cap - A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. - Elisabetta Manduchi - OTHER: Adjusted from MGED Ontology - loess scale group transformation two-channel + 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 - + - - - loess global transformation one-channel - Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. + + + specimen collection device - A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. - Elisabetta Manduchi - OTHER: Editor's generalization based on MGED Ontology term - loess global transformation one-channel + A container used to collect a specimen. + https://orcid.org/0000-0002-8844-9165 + specimen collection device - + - - - split-scale transformation - This type of transformation is typically used in flow cytometry + + + 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 split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - split-scale transformation + 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 - + - - - loess global transformation two-channel - Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. + + + specimen collection swab stick + A swab stick allows a worker to collect samples without touching the inside of the bag - A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. - Elisabetta Manduchi - OTHER: Editor's generalization based on MGED Ontology term - loess global transformation two-channel + 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 + sponge stick + polyprobe + sponge probe + sponge-stick + https://medical-dictionary.thefreedictionary.com/swab + specimen collection swab stick - + - - - - - - - - - sine transformation - sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc. + + + cotton swab - A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. - Elisabetta Manduchi - WEB: http://mathworld.wolfram.com/Sine.html - sine transformation + 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 - + - - + + - - + + - cosine transformation - cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc. + drag swab - 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 - WEB: http://mathworld.wolfram.com/Cosine.html - cosine transformation + 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 - + - - - loess group transformation one-channel - A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. + + + pre-moistened swab stick - A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. - Elisabetta Manduchi - OTHER: Editor's generalization based on MGED Ontology term - loess group transformation one-channel + 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 - + - - - loess group transformation two-channel - A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. + + + 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 loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. - Elisabetta Manduchi - OTHER: Editor's generalization based on MGED Ontology term - loess group transformation two-channel + 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 - + - - - homogeneous polynomial transformation - a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables. - - A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. - Elisabetta Manduchi - WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html - homogeneous polynomial transformation + + + 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 - + - - - - - - - - - linlog transformation - This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. - - 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 - PMID: 16646782 - linlog transformation + + + 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 - + - - - - - - - - - variance stabilizing transformation - This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536. - - A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper. - Elisabetta Manduchi - James Malone - Melanie Courtot - variance stabilising transformation - PMID: 12169536 - variance stabilizing transformation + + + 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 - + - - - loess global transformation - - A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - OTHER: Editor's generalization based on MGED Ontology term - loess global transformation + + + 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 - + - - - loess group transformation - - A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - OTHER: Editor's generalization based on MGED Ontology term - loess group transformation + + + 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 - + - - - - - - - - - - - - - - - loess scale group transformation - - A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. - Elisabetta Manduchi - James Malone - Melanie Courtot - OTHER: Editor's generalization based on MGED Ontology term - loess scale group transformation + + + 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 - + - - - - - - - - - total intensity transformation single - This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). - - A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. - Elisabetta Manduchi - Helen Parkinson - James Malone - Melanie Courtot - 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 + + + 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 - + - - - - - - - - - total intensity transformation paired - This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. - - 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 - 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 + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - quantile transformation - This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. - - A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - quantile transformation + + + 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 - + - - - - - - - - - mean centering - This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered. - - 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 - mean centring - PERSON: Elisabetta Manduchi - mean centering + + + 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 - + - - - - - - - - - median centering - This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered. - - 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 - median centring - PERSON: Elisabetta Manduchi - median centering + + + 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 - + - - - differential expression analysis objective - Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software - - A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - differential expression analysis objective + + + 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 - + - - - - - - - - - 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 method + + + 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 - + - - - - - - - - - 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 - - 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 + + + 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 - + - - - - - - - - - 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 - jackknifing - http://en.wikipedia.org/wiki/Resampling_%28statistics%29 - jackknifing method + + + 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 - + - - - - - - - - - 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. - - 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 - boostrapping + + + A specimen collection process that has the objective of collecting arthropods as specimens. + John Judkins + field population catch + collection of arthropods + MIRO:30000044 + https://github.com/obi-ontology/obi/issues/1217 + arthropod specimen collection process - + - - - - - - - - - - - - - - - - - - - - - - - - - - - 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) - - 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 - Philippe Rocca-Serra - Helen Parkinson - Benjamini and Hochberg false discovery rate correction method + + + 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 - + - - - - - - - - - pareto scaling - - A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. - Elisabetta Manduchi - Philippe Rocca-Serra - PMID:16762068 - pareto scaling + + + 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 - + - - - modular decomposition - - Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. - Tina Hernandez-Boussard - editor - modular decomposition + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - 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 - James Malone - Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/K-means - k-means clustering + + + 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 - + - - - - - - - - - - - - - - - - - hierarchical clustering - - A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). - James Malone - WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering - hierarchical clustering + + + 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 - + - - - average linkage hierarchical clustering - - An average 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 average distance between objects from the first cluster and objects from the second cluster. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - average linkage hierarchical clustering + + + An arthropod specimen collection process meant to collect live specimens. + John Judkins + catch of live specimens + VSMO:0001445 + MIRO:30000044 + https://github.com/obi-ontology/obi/issues/1217 + live arthropod specimen collection process - + - - - complete linkage hierarchical clustering - - an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - complete linkage hierarchical clustering + + + A device designed to catch arthropods. + John Judkins + trap catch + MIRO:30000011 + https://github.com/obi-ontology/obi/issues/1217 + arthropod trap - + - - - 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 - PERSON: Elisabetta Manduchi - single linkage hierarchical clustering + + + 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 - + - - - - - - - - - - - - - - + + + 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 + + + + + + + + + An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. + John Judkins + barrier catch + IRO:0000017 + https://github.com/obi-ontology/obi/issues/1217 + barrier trap + + + + + + + + - - + + + A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. + John Judkins + BG-Counter trap catch + IRO:0000143 + https://github.com/obi-ontology/obi/issues/1217 + BG-Counter + + + + + + + + - - + + - 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) - - 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 - Philippe Rocca-Serra - Helen Parkinson - Benjamini and Yekutieli false discovery rate correction method + 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 + BG-Sentinel trap catch + IRO:0000028 + VSMO:0001906 + https://github.com/obi-ontology/obi/issues/1217 + BG-Sentinel trap - + - - - - - - - - - - - - - - - - - dimensionality reduction - - A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - data projection - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - dimensionality reduction + + + A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. + John Judkins + CDC light trap catch + IRO:0000163 + https://github.com/obi-ontology/obi/issues/1217 + Centers for Disease Control and Prevention light trap - + - - - principal components analysis dimensionality reduction - - A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - pca data reduction - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - principal components analysis dimensionality reduction + + + 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 - + - - - probabilistic algorithm - - A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. - James Malone - PERSON: James Malone - probabilistic algorithm + + + 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 catch + IRO:0000029 + VSMO:0001295 + https://github.com/obi-ontology/obi/issues/1217 + encephalitis virus surveillance trap - + - - - expectation maximization - - EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. - James Malone - PERSON: James Malone - expectation maximization + + + An arthropod trap that is designed to collect gravid female arthropods or their eggs. + John Judkins + gravid trap catch + IRO:0000030 + https://github.com/obi-ontology/obi/issues/1217 + gravid trap - + - - - global modularity calculation - - A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. - Richard Scheuermann - PERSON: Richard Scheuermann - global modularity calculation + + + An arthropod trap that uses light as an attractant. + John Judkins + light trap catch + MIRO:30000065 + https://github.com/obi-ontology/obi/issues/1217 + light trap - + - - - dye swap merge - - A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. - Elisabetta Manduchi - James Malone - PERSON: Elisabetta Manduchi - PERSON: James Malone - dye swap merge + + + A light trap designed to be placed inside a building. + John Judkins + indoor light trap catch + MIRO:30000009 + https://github.com/obi-ontology/obi/issues/1217 + light trap for indoor use - + - - - - - - - - - - - - - - - - - moving average - The moving average is often used to handle data from tiling arrays. - - 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 - PERSON: Elisabetta Manduchi - PERSON: Helen Parkinson - moving average + + + A light trap designed to be placed outside a building. + John Judkins + outdoor light trap catch + MIRO:30000010 + https://github.com/obi-ontology/obi/issues/1217 + light trap for outdoor use - + - - - - - - - - - replicate analysis - Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. - - A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. - Elisabetta Manduchi - Helen Parkinson - PERSON: Helen Parkinson - PERSON:Elisabetta Manduchi - replicate analysis + + + 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 + mosquito magnet pro catch + IRO:0000022 + https://github.com/obi-ontology/obi/issues/1217 + Mosquito Magnet trap - + - - - - - - - - - b cell epitope prediction - - A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. - Helen Parkinson - PERSON: Helen Parkinson - b cell epitope prediction + + + A gravid trap consisting of an arthropod attractant and adhesive surface. + John Judkins + IRO:0000140 + https://github.com/obi-ontology/obi/issues/1217 + MosquiTRAP - + - - - - - - - - - mhc binding prediction - - An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. - Helen Parkinson - PERSON: Helen Parkinson - mhc binding prediction + + + 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 catch + IRO:0000031 + https://github.com/obi-ontology/obi/issues/1217 + New Jersey light trap - + - - - - - - - - - t cell epitope prediction - - A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. - Helen Parkinson - PERSON: Helen Parkinson - t cell epitope prediction + + + 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 - + - - - data imputation - - Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. - Monnie McGee - ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. - data imputation + + + 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 catch + MIRO:30000020 + https://github.com/obi-ontology/obi/issues/1217 + outlet window trap - + - - - - - - - - - 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: Tina Hernandez-Boussard - PERSON: Tina Boussard - continuum mass spectrum + + + 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 - + - - - - - - - - - characteristic path length calculation - - Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices - PERSON: Tina Hernandez-Boussard - PERSON: Tina Hernandez-Boussard - characteristic path length calculation + + + 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 - + - - - - - - - - - centroid mass spectrum - - 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 - centroid mass spectrum + + + 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 - + - - - - - - - - - - - - - - - - - - - - - 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 - - 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 + + + 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 + + -The 'editor preferred term' should be removed - Person:Helen Parkinson - Philippe Rocca-Serra - WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method - Holm-Bonferroni family-wise error rate correction method + + + + + + 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 - + - - - edge weighting - - Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. - Tina Hernandez-Boussard - editor - was classified under algorithm class which is not acceptable super-class -TO BE DEALT WITH STILL BY RICHARD. JAMES - edge weighting + + + 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 - + - - - - - - - - - loess transformation - - A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. - Elisabetta Manduchi - James Malone - Melanie Courtot - Philippe Rocca-Serra - OTHER: Editor's generalization based on MGED Ontology term - loess transformation + + + 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 + #1090 + population based design + + + + + + + + - + + - - + + - - + + - + - - - curve fitting data transformation - - A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. - Elisabetta Manduchi - James Malone - Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Curve_fitting - curve fitting data transformation + + 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 - + - - - - - - - - + - - - - + + + + + + + + + + + + + - 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. - 2011-03-31: [PRS]. -creating a defined class by specifying the necessary output of dt -allows correct classification of FWER dt - 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 - family wise error rate correction method + 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 - + - - - submatrix extraction - When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set. - - A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) - Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix. - Elisabetta Manduchi - James Malone - Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Submatrix - submatrix extraction + + + 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 - + - - - row submatrix extraction - When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set. - - A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. - Elisabetta Manduchi - James Malone - Melanie Courtot - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - row submatrix extraction + + + 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 - + - - - column submatrix extraction - When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set. - - A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. - Elisabetta Manduchi - James Malone - Melanie Courtot - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - column submatrix extraction + + + 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 - + - - - - - - - - - - - - - - - gating - - Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. - James Malone - Josef Spidlen - Melanie Courtot - Richard Scheuermann - Ryan Brinkman - PERSON: James Malone - PERSON: Josef Spidlen - PERSON: Richard Scheuermann - PERSON: Ryan Brinkman - PERSON:Melanie Courtot - gating + + + 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 - + - - - descriptive statistical calculation objective - - A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. - Elisabetta Manduchi - James Malone - Melanie Courtot - Monnie McGee - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - PERSON: Monnie McGee - descriptive statistical calculation objective + + + 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 - + - - + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + - - + + + + + + + + + + + + - - + + + 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 + + + + + + + + - - + + + + + + + + + + + + - - + + + 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 + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + - arithmetic mean calculation - - 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 - 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) - arithmetic mean calculation + 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 - + - - - network analysis - - 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 - PERSON: Richard Scheuermann - network analysis + + + 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 - + - - - 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 - sequence analysis objective + + + + + + + + + + + + + + + + + + + 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 - + - - - - - - - - - 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 - longitudinal data analysis - longitudinal data analysis + + + 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 - + - - - survival analysis objective - 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 - survival analysis objective + + + 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 - + - - - - - - - - - mass spectrometry analysis - - A data transformation which has the objective of spectrum analysis. - mass spectrometry analysis + + + 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 - + - - - - - - - - - spread calculation data transformation - - A spread calculation is a data transformation that has objective spread calculation. - James Malone - EDITOR - spread calculation data transformation + + + 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 + + + + + + + - - - - + + + + + + + + + - 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 - Kaplan Meier + 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 - + - - - - - - - - - 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 - 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. - multiple testing correction method + + + 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 - - - - - 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 - inter-rater reliability objective + + + 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 - + - - - - - - - - - - - - - - - - - - - - - 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 - 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 - Westfall and Young FWER correction - Westfall and Young family wise error rate correction + + + 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 - + - - - polynomial transformation - a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 -variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables - - A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. - Elisabetta Manduchi - WEB: http://mathworld.wolfram.com/Polynomial.html - polynomial transformation + + + 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 - + - - - - - - - - - logarithmic transformation - - A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. - Elisabetta Manduchi - WEB: http://en.wikipedia.org/wiki/Logarithm - logarithmic transformation + + + 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 - + - - - - - - - - - exponential transformation - - An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. - Elisabetta Manduchi - WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function - WEB: http://en.wikipedia.org/wiki/Exponential_function - exponential transformation + + + 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 - + - - - 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 + + + 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 - + - - - - - - - - - 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 - SIMCA - WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies - soft independent modeling of class analogy analysis + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - discriminant function analysis - - Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. - Tina Hernandez-Boussard - WEB: http://www.statsoft.com/textbook/stdiscan.html - discriminant function analysis + + + 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 - + - - - - - - - - - canonical variate analysis - - canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. - Tina Hernandez-Boussard - CVA - WEB: http://en.wikipedia.org/wiki/Canonical_analysis - canonical variate analysis + + + 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 resting of adult arthropods for collection - + - - - - - - - - - - - - - - - - - - - - - - - linear discriminant functional analysis - - Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. - Tina Hernandez-Boussard - PERSON: Tina Hernandez-Boussard - linear discriminant functional analysis + + + 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 - + - - - regression analysis method - - Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. - Tina Hernandez-Boussard - BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 - regression analysis method + + + 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 - + - - - multiple linear regression analysis - - multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as - Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon -where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. - Tina Hernandez-Boussard - WEB:http://en.wikipedia.org/wiki/Linear_regression - multiple linear regression analysis + + + 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 - + - - - + + + - - - - - + + + + + + - - principal component regression - - The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. - Tina Hernandez-Boussard - WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html - principal component regression + + An assay that measures ferritin + James A. Overton, ORCID:0000-0001-5139-5557 + OBI + ferritin assay - + - - - partial least square regression analysis - - Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that -Y = b0 + b1X1 + b2X2 + ... + bpXp -In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. - Tina Hernandez-Boussard - PLS-RA - ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263. - partial least square regression analysis + + + + + + + + + + + + + + + + + + An assay that measures fibrinogen + James A. Overton, ORCID:0000-0001-5139-5558 + OBI + fibrinogen assay - + - - - discriminant analysis - - Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. - Tina Hernandez-Boussard - WEB: http://www.statsoft.com/textbook/stdiscan.html - discriminant analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An analyte assay that measures the abundance of iron + James A. Overton, ORCID:0000-0001-5139-5559 + OBI + iron assay - + - - - 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. - James Malone - PLS-DA - WEB: http://www.camo.com/rt/Resources/pls-da.html - partial least square discriminant analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An analyte assay that measures the abundance of ionized calcium + James A. Overton, ORCID:0000-0001-5139-5561 + OBI + ionized calcium assay - + - - - - - - - - - eh transformation - This type of transformation is typically used in flow cytometry. - - An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - eh transformation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An analyte assay that measures the abundance of transferrin + James A. Overton, ORCID:0000-0001-5139-5562 + OBI + transferrin assay - + - - - + + - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - b transformation - This type of transformation is typically used in flow cytometry. - - A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - b transformation + + An analyte assay that measures the abundance of uric acid + James A. Overton, ORCID:0000-0001-5139-5563 + OBI + uric acid assay - + - - - - - - - - - s transformation - This type of transformation is typically used in flow cytometry. - - An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. - Elisabetta Manduchi - Joseph Spliden - Ryan Brinkman - WEB: http://flowcyt.sourceforge.net/gating/latest.pdf - s transformation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An analyte assay that measures the abundance of globulin + James A. Overton, ORCID:0000-0001-5139-5564 + OBI + globulin assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - visualization - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - PERSON: Tina Boussard - Possible future hierarchy might include this: -information_encoding ->data_encoding ->>image_encoding - data visualization + + + + + + + + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of myelocytes + James A. Overton, ORCID:0000-0001-5139-5565 + OBI + myelocyte assay - + - - - - - - - - - - - - - - - similarity calculation - - A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - similarity calculation + + + + + + + + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of metamyelocytes + James A. Overton, ORCID:0000-0001-5139-5566 + OBI + metamyelocyte assay - + - - - euclidean distance calculation - - An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - euclidean distance calculation + + + + + + + + + + + + + + + + + + A cytometry assay that measures the proportion of red blood cells + James A. Overton, ORCID:0000-0001-5139-5567 + OBI + hematocrit assay - + - - - pearson correlation coefficient calculation - - A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. - Elisabetta Manduchi - PERSON: Elisabetta Manduchi - WEB: http://en.wikipedia.org/wiki/Correlation - pearson correlation coefficient calculation + + + + + + + + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of promyelocytes + James A. Overton, ORCID:0000-0001-5139-5568 + OBI + promyelocyte assay - + - - - - - - - - - loess fitting - - 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 - ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. - loess fitting + + + + + + + + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of basophils + James A. Overton, ORCID:0000-0001-5139-5569 + OBI + basophil assay - + - - - + + + - - - - - + + + + + + - - - - - - - - mode calculation - - A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. - James Malone - Monnie McGee - PERSON: James Malone - PERSON: Monnie McGee - From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) - mode calculation + + A cytometry assay that measures the abundance and/or characteristics of neutrophils + James A. Overton, ORCID:0000-0001-5139-5570 + OBI + neutrophil assay - + - - - - - - - - - quantile calculation - - A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. - Monnie McGee - WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html - quantile calculation + + + + + + + + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of eosinophils + James A. Overton, ORCID:0000-0001-5139-5571 + OBI + eosinophil assay - + - - - + + + - - - - - + + + + + + - - - - - - - - median calculation - - A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values. - James Malone - Monnie McGee - PERSON: James Malone - PERSON: Monnie McGee - From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) - median calculation + + A cytometry assay that measures the abundance and/or characteristics of lymphocytes + James A. Overton, ORCID:0000-0001-5139-5572 + OBI + lymphocyte assay - + - - - - - - - - - - - - - - - variance calculation - - A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. - Monnie McGee - PERSON: Monnie McGee - From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008) - variance calculation + + + + + + + + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of monocytes + James A. Overton, ORCID:0000-0001-5139-5573 + OBI + monocyte assay - + - - - - - - - - - - - - - - - standard deviation calculation - - A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. - Monnie McGee - PERSON: Monnie McGee - From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) - standard deviation calculation + + + + + + + + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of reticulocytes + James A. Overton, ORCID:0000-0001-5139-5574 + OBI + reticulocyte assay - + - - - - - - - - - - - - - - - interquartile-range calculation - - The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. - Monnie McGee - PERSON: Monnie McGee - From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) - interquartile-range calculation + + + + + + + + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of macrophages + James A. Overton, ORCID:0000-0001-5139-5577 + OBI + macrophage assay - + - - - + + + - + + + + + + + + + + + A cytometry assay that measures the abundance and/or characteristics of platelets + James A. Overton, ORCID:0000-0001-5139-5578 + OBI + platelet assay + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - skewness calculation + + + 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 skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment - Monnie McGee - WEB: http://www.riskglossary.com/link/skewness.htm - From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) - skewness calculation + 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 + + + + + + + + + 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 + + + + + + + + - - - - + + + + + + + + + - - + + + + + + + + + + + + - kurtosis calculation + 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 kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html - Monnie McGee - WEB: http://davidmlane.com/hyperstat/A53638.html - From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) - kurtosis calculation + 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 - + - - + + - - + + + + + + + + + + + + + + + + + + - data combination - - 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 - editor - data combination + + + + + + + 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 - + - - - network graph construction - - A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. - Richard Scheuermann - PERSON: Richard Scheuermann - network graph construction + + + + + + + + + + + + + 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 - + - - - weighted network graph construction - - A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. - Richard Scheuermann - PERSON: Richard Scheuermann - weighted network graph construction + + + 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 - + - - - directed network graph construction - - A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. - Richard Scheuermann - PERSON: Richard Scheuermann - directed network graph construction + + + 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 - + - - - node quality calculation - - A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. - Richard Scheuermann - PERSON: Richard Scheuermann - node quality calculation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - - node degree calculation - - A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node. - Richard Scheuermann - PERSON: Richard Scheuermann - node degree calculation + + + + + + + + + + + + + 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 - + - - - quantitative node degree calculation - - A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. - Richard Scheuermann - PERSON: Richard Scheuermann - quantitative node degree calculation + + + + A material entity that represents generations of a primary culture. + PERSON: Susanna Sansone + GROUP: OBI Biomaterial Branch + + obsolete_cell line cell + true - + - - - node in-degree calculation - - A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node. - Richard Scheuermann - PERSON: Richard Scheuermann - node in-degree calculation + + + + 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 - + - - - node out-degree calculation - - A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. - Richard Scheuermann - PERSON: Richard Scheuermann - node out-degree calculation + + + + + + + + + + + + + + + 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 - + - - - node shortest path identification - - A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. - Richard Scheuermann - PERSON: Richard Scheuermann - node shortest path identification + + + + + + + + + + + + + + + + + + + + + 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 - + - - - edge quality calculation - - A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. - Richard Scheuermann - PERSON: Richard Scheuermann - edge quality calculation + + + + + + + + + + + + + + + + + + 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. + - + - - - edge betweenness calculation - - An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. - Richard Scheuermann - PERSON: Richard Scheuermann - edge betweenness calculation + + + 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 - + - - - network subgraph quality calculation - - A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. - Richard Scheuermann - PERSON: Richard Scheuermann - network subgraph quality calculation + + + 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 - + - - - subgraph degree calculation - - A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - subgraph degree calculation + + + 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 - + - - - quantitative subgraph degree calculation - - A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - quantitative subgraph degree calculation + + + + + + + + + + + + + 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 - + - - - 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 - mathematical feature + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + - - + + - log base + + + + + + + bronchial alveolar lavage + solution containing lung derived T cells, eosinophils, and TNFa. - 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 + 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 - + - - - subgraph in-degree calculation - - A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - subgraph in-degree calculation + + + + 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 - + - - - subgraph out-degree calculation - - A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. - Richard Scheuermann - PERSON: Richard Scheuermann - subgraph out-degree calculation + + + + + + + + + glucose in solution + Glucose present in blood + + A scattered aggregate of glucose molecules in a liquid + PERSON: Jie Zheng + glucose molecules + glucose in solution - + - - - intra subgraph connectivity calculation - - A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - PERSON: Richard Scheuermann - intra subgraph connectivity calculation + Ryan Brinkman + Tina Hernandez-Boussard + data analysis + data processing + Branch editors + data transformation - + - - - subgraph modularity calculation - - A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. - Richard Scheuermann - PERSON: Richard Scheuermann - subgraph modularity calculation + + + + + + + + + + + + + + + + + + + + + + + geometric mean calculation + 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). + geometric mean calculation - + - - - network graph quality calculation - - A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole. - Richard Scheuermann - PERSON: Richard Scheuermann - network graph quality calculation + + + + + + + + + logistic-log curve fitting + Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve. + + A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). + Elisabetta Manduchi + James Malone + Melanie Courtot + Ryan Brinkman + ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 + logistic-log curve fitting - + - + - + - unit-variance scaling - - A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. + logit-log curve fitting + Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively. + + A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points. + The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model. Elisabetta Manduchi - Philippe Rocca-Serra - autoscaling - PMID:16762068 - unit-variance scaling + James Malone + Melanie Courtot + Ryan Brinkman + ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 + logit-log curve fitting - + - + - 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. + + + + + + + log-log curve fitting + Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. + + A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. + Elisabetta Manduchi + James Malone + Melanie Courtot + Ryan Brinkman + ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 + log-log curve fitting + + + + + + + + + feature extraction objective - 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. + 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 - Philippe Rocca-Serra - PERSON: Elisabetta Manduchi - MA transformation + James Malone + TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction + feature extraction objective - + - - + + + + + + + + + + + + + + + + - - + + - 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 - exponential base + biexponential transformation + This type of transformation is typically used in flow cytometry. + + A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + biexponential transformation - + - - + + - - + + - 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 - polynomial degree + box-cox transformation + + A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. + Ryan Brinkman + ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246. + box-cox transformation - + - - + + - - + + - 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 - number of variables + hyperlog transformation + This type of transformation is typically used in flow cytometry + + A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42." + http://flowcyt.sourceforge.net/gating/latest.pdf + hyperlog transformation - + - - - 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 - James Malone - bottom-up hierarchical clustering - PERSON: Elisabetta Manduchi - agglomerative hierarchical clustering + + + loess scale group transformation one-channel + Loess scale group normalization applied to data from two one-channel expression microarray assays. + + A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. + Elisabetta Manduchi + OTHER: Editor's adjustment based on MGED Ontology term + loess scale group transformation one-channel - + - - - 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 - James Malone - top-down hierarchical clustering - PERSON: Elisabetta Manduchi - divisive hierarchical clustering + + + + + + + + + logical transformation + This type of transformation is typically used in flow cytometry. + + A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + logical transformation - + - - - data partitioning - - Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. - James Malone - PERSON: Melanie Courtot - PERSON: Richard Scheuermann - PERSON: Ryan Brinkman - data partitioning + + + loess scale group transformation two-channel + Loess scale group normalization applied to data from a two-channel expression microarray assay. + + A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. + Elisabetta Manduchi + OTHER: Adjusted from MGED Ontology + loess scale group transformation two-channel - + - - - 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 - Richard H. Scheuermann - PERSON: Richard H. Scheuermann - data vector reduction objective + + + loess global transformation one-channel + Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. + + A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. + Elisabetta Manduchi + OTHER: Editor's generalization based on MGED Ontology term + loess global transformation one-channel - + - + - - - - - - - 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 - gFWER correction - 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 + split-scale transformation + This type of transformation is typically used in flow cytometry + + A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + split-scale transformation - + - - - - - - - - - - - - - - - - - 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 - QNFP - 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 + + + loess global transformation two-channel + Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. + + A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. + Elisabetta Manduchi + OTHER: Editor's generalization based on MGED Ontology term + loess global transformation two-channel - + - + - + - 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 - TPPFP correction method - 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 + sine transformation + sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc. + + A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. + Elisabetta Manduchi + WEB: http://mathworld.wolfram.com/Sine.html + sine transformation - + - - - - - - - + - - - - - - - + - 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. . - 2011-03-31: [PRS]. -creating a defined class by specifying the necessary output of dt -allows correct classification of FDR dt - 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 - false discovery rate correction method + cosine transformation + cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc. + + 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 + WEB: http://mathworld.wolfram.com/Cosine.html + cosine transformation - + - + + + loess group transformation one-channel + A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. + + A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. + Elisabetta Manduchi + OTHER: Editor's generalization based on MGED Ontology term + loess group transformation one-channel + + + + + + + + + loess group transformation two-channel + A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. + + A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. + Elisabetta Manduchi + OTHER: Editor's generalization based on MGED Ontology term + loess group transformation two-channel + + + + + + + + + homogeneous polynomial transformation + a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables. + + A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree. + Elisabetta Manduchi + WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html + homogeneous polynomial transformation + + + + + + + - - - - - - - - - - - - + + + + - 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 - PEFP correction method - 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 + linlog transformation + This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782. + + 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 + PMID: 16646782 + linlog transformation - + - + - - - - - - - - - - - - + + + + - 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 - QPFP correction method - 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 + variance stabilizing transformation + This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536. + + A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper. + Elisabetta Manduchi + James Malone + Melanie Courtot + variance stabilising transformation + PMID: 12169536 + variance stabilizing transformation - + - - - data transformation objective - normalize objective + + + loess global transformation - An objective specification to transformation input data into output data - Modified definition in 2013 Philly OBI workshop + A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation. + Elisabetta Manduchi James Malone - PERSON: James Malone - data transformation objective + Melanie Courtot + Philippe Rocca-Serra + OTHER: Editor's generalization based on MGED Ontology term + loess global transformation - + - - - data normalization objective - Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. + + + loess group transformation - 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 + A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. + Elisabetta Manduchi James Malone - PERSON: Elisabetta Manduchi - PERSON: Helen Parkinson - PERSON: James Malone - data normalization objective + Melanie Courtot + Philippe Rocca-Serra + OTHER: Editor's generalization based on MGED Ontology term + loess group transformation - + - - - correction objective - Type I error correction - - 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 + + + + + + + + + + + + + + + loess scale group transformation + + A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling. + Elisabetta Manduchi James Malone - PERSON: James Malone - PERSON: Melanie Courtot - correction objective + Melanie Courtot + OTHER: Editor's generalization based on MGED Ontology term + loess scale group transformation - + - - - - - - - - - - - - - - - + - normalization data transformation - - A normalization data transformation is a data transformation that has objective normalization. - James Malone - PERSON: James Malone - normalization data transformation + + + + + + + total intensity transformation single + This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)). + + A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice. + Elisabetta Manduchi + Helen Parkinson + James Malone + Melanie Courtot + 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 - + - - + + + + + + + + + total intensity transformation paired + This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. + + 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 + 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 + + + + + + + + + - + - + - + - + - - - averaging data transformation - - An averaging data transformation is a data transformation that has objective averaging. - James Malone - PERSON: James Malone - averaging data transformation + + + + + + + + quantile transformation + This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. + + A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + quantile transformation - + - - + + + - + - - - partitioning data transformation - - A partitioning data transformation is a data transformation that has objective partitioning. - James Malone - PERSON: James Malone - partitioning data transformation + + mean centering + This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered. + + 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 + mean centring + PERSON: Elisabetta Manduchi + mean centering - + - - - partitioning objective - A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. + + + + + + + + + median centering + This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered. - 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 - James Malone - PERSON: Elisabetta Manduchi - partitioning objective + 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 + median centring + PERSON: Elisabetta Manduchi + median centering - + - - - 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 - James Malone - PERSON: Elisabetta Manduchi - background correction objective + + + differential expression analysis objective + Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software + + A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + differential expression analysis objective - + - - - 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 - James Malone - PERSON: Elisabetta Manduchi - curve fitting objective + + + + + + + + + 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 method - + - - - - - - - - - - - - - - - + - 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 - PERSON: James Malone - class discovery data transformation + + + + + + + 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 + + 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 - + - + - + - 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 + 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 + jackknifing + http://en.wikipedia.org/wiki/Resampling_%28statistics%29 + jackknifing method - + - - - center calculation objective - A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. - - 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 - center calculation objective + + + + + + + + + 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. + + 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 + boostrapping - + - - - class discovery objective - - 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 - discriminant analysis objective - unsupervised classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone - class discovery objective + + + + + + + + + + + + + + + + + + + + + + + + + + + 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) + + 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 + Philippe Rocca-Serra + Helen Parkinson + Benjamini and Hochberg false discovery rate correction method - + - - - class prediction objective - - 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 - supervised classification objective - PERSON: Elisabetta Manduchi - PERSON: James Malone - class prediction objective + + + + + + + + + pareto scaling + + A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable. + Elisabetta Manduchi + Philippe Rocca-Serra + PMID:16762068 + pareto scaling - + - - - spread calculation objective - 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 - Awaiting English definition from Monnie McGee - James Malone - Person:Helen Parkinson - spread calculation objective + + + modular decomposition + + Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins. + Tina Hernandez-Boussard + editor + modular decomposition - + - - + + + - + - + - + - + - - - center calculation data transformation - - A center calculation data transformation is a data transformation that has objective of center calculation. - James Malone - PERSON: James Malone - center calculation data transformation + + + + + + + + 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 + James Malone + Philippe Rocca-Serra + WEB: http://en.wikipedia.org/wiki/K-means + k-means clustering - + - - + + + - + - + - + - + - - - data vector reduction data transformation - - A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k. + + hierarchical clustering + + A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). James Malone - PERSON: James Malone - data vector reduction data transformation + WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering + hierarchical clustering - + - - - scaling objective - 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 - Awaiting English definition from Monnie McGee - James Malone - Person:Helen Parkinson - scaling objective + + + average linkage hierarchical clustering + + An average 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 average distance between objects from the first cluster and objects from the second cluster. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + average linkage hierarchical clustering - + - - - - - - - - - - - - - - - - - descriptive statistical calculation data transformation - - A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. - James Malone - PERSON: James Malone - descriptive statistical calculation data transformation + + + complete linkage hierarchical clustering + + an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + complete linkage hierarchical clustering - + - - + + + 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 + PERSON: Elisabetta Manduchi + single linkage hierarchical clustering + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + + 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) + + 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 + Philippe Rocca-Serra + Helen Parkinson + Benjamini and Yekutieli false discovery rate correction method + + + + + + + - scaling data transformation + + + + + + + + + + + + + + + dimensionality reduction - A scaling data transformation is a data transformation that has objective scaling. + A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. + Elisabetta Manduchi James Malone + Melanie Courtot + Philippe Rocca-Serra + data projection + PERSON: Elisabetta Manduchi PERSON: James Malone - scaling data transformation + PERSON: Melanie Courtot + dimensionality reduction - + - - - error correction objective - 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 - error correction objective + + + principal components analysis dimensionality reduction + + A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. + Elisabetta Manduchi + James Malone + Melanie Courtot + Philippe Rocca-Serra + pca data reduction + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + principal components analysis dimensionality reduction - + - - - - - - - + - sequence analysis data transformation + probabilistic algorithm - 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. + A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. James Malone - EDITOR - sequence analysis data transformation + PERSON: James Malone + probabilistic algorithm - + - - - cross validation objective - - 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. + + + expectation maximization + + EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function. James Malone - rotation estimation objective - WEB: http://en.wikipedia.org/wiki/Cross_validation - cross validation objective + PERSON: James Malone + expectation maximization - + - - - 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 - merging objective + + + global modularity calculation + + A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network. + Richard Scheuermann + PERSON: Richard Scheuermann + global modularity calculation - + - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + dye swap merge + + A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. + Elisabetta Manduchi + James Malone + PERSON: Elisabetta Manduchi + PERSON: James Malone + dye swap merge - + - - - - - - - - + + - - - - + + + + + + + + + + + + - 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 + moving average + The moving average is often used to handle data from tiling arrays. + + 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 + PERSON: Elisabetta Manduchi + PERSON: Helen Parkinson + moving average - + - - - - - - - - - - - - - - - + + - - + + - 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 + replicate analysis + Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. + + A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc. + Elisabetta Manduchi + Helen Parkinson + PERSON: Helen Parkinson + PERSON:Elisabetta Manduchi + replicate analysis - + - - - - - - - - - - - - - - - + + - - + + - background corrected data visualization + b cell epitope prediction - 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 B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. + Helen Parkinson + PERSON: Helen Parkinson + b cell epitope prediction - + - - + + + - + - - - survival analysis data transformation - - A data transformation which has the objective of performing survival analysis. - James Malone - PERSON: James Malone - survival analysis data transformation + + mhc binding prediction + + An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule. + Helen Parkinson + PERSON: Helen Parkinson + mhc binding prediction - + - + - + - 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 - - - - - - - - - correlation study objective + t cell epitope prediction - 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 T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. + Helen Parkinson + PERSON: Helen Parkinson + t cell epitope prediction - + - - - 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 + + + data imputation + + Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. + Monnie McGee + ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. + data imputation - + - + @@ -68615,21 +68340,20 @@ 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 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). + 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: Tina Boussard - PERSON: Tina Boussard - tandem mass spectrometry + PERSON: Tina Hernandez-Boussard + PERSON: Tina Boussard + continuum mass spectrum - + - + @@ -68637,293 +68361,300 @@ class labels for these objects. The resulting predictor can be used to attach cl - gas chromatography mass spectrometry + characteristic path length calculation - 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 + Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices + PERSON: Tina Hernandez-Boussard + PERSON: Tina Hernandez-Boussard + characteristic path length calculation - + - + - + - chi square test + centroid mass spectrum - 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 + 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 + centroid mass spectrum - + - + - 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 + + + + + + + + + + + + + + + + + + + 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 + + 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 + Philippe Rocca-Serra + WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method + Holm-Bonferroni family-wise error rate correction method - + - - - 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 + + + edge weighting + + Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network. + Tina Hernandez-Boussard + editor + was classified under algorithm class which is not acceptable super-class +TO BE DEALT WITH STILL BY RICHARD. JAMES + edge weighting - + - - - 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. + + + + + + + + + loess transformation + + A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves. + Elisabetta Manduchi + James Malone + Melanie Courtot Philippe Rocca-Serra - OBI branch derived - observation design - - - - - - - - - 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) - true + OTHER: Editor's generalization based on MGED Ontology term + loess transformation - + - + - - + - - - - - - - - - - - - + + - + + + + + - pool of specimens - - 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 - pool of specimens + + curve fitting data transformation + + A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints. + Elisabetta Manduchi + James Malone + Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Curve_fitting + curve fitting data transformation - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - chemical solution - 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. + + + + + + + + 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. + 2011-03-31: [PRS]. +creating a defined class by specifying the necessary output of dt +allows correct classification of FWER dt + 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 + family wise error rate correction method + + + + + + + + + submatrix extraction + When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set. - 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 - liquid chemical solution - GROUP: OBI Biomaterial Branch - chemical solution + A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) + Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix. + Elisabetta Manduchi + James Malone + Melanie Courtot + WEB: http://en.wikipedia.org/wiki/Submatrix + submatrix extraction - + - - - 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 - buffer role + + + row submatrix extraction + When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set. + + A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows. + Elisabetta Manduchi + James Malone + Melanie Courtot + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + row submatrix extraction - + - - - - - - - - - - - - - - - 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) - solvent role + + + column submatrix extraction + When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set. + + A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns. + Elisabetta Manduchi + James Malone + Melanie Courtot + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + column submatrix extraction - + - - + + - - + + - - + + - 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. + gating - 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) - solute role + Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. + James Malone + Josef Spidlen + Melanie Courtot + Richard Scheuermann + Ryan Brinkman + PERSON: James Malone + PERSON: Josef Spidlen + PERSON: Richard Scheuermann + PERSON: Ryan Brinkman + PERSON:Melanie Courtot + gating - + - - + + + descriptive statistical calculation objective + + A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. + Elisabetta Manduchi + James Malone + Melanie Courtot + Monnie McGee + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + PERSON: Monnie McGee + descriptive statistical calculation objective + + + + + + + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + @@ -68932,6534 +68663,6667 @@ determinations of compounds. - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - + + - 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 + arithmetic mean calculation + + 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 - SCGE assay - single cell gel electrophoresis assay - PMID:7686265 - comet assay + 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) + arithmetic mean calculation - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 + + + network analysis + + 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 + PERSON: Richard Scheuermann + network analysis - + - - - 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 - - obsolete_liver - true + + + 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 + sequence analysis objective - + - - - 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 - - obsolete_adipose tissue - true + + + + + + + + + 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 + longitudinal data analysis + longitudinal data analysis - + - - - - - - - - - - - - - denatured polymer + + + survival analysis objective + Kaplan meier data transformation - Is a polymer which has lost secondary or tertiary structure - PERSON: Alan Ruttenberg - http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 - denatured polymer + 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 - + - + - - - - - - - - - + + + + - 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 - OBI Biomaterial - decapitated organism + + mass spectrometry analysis + + A data transformation which has the objective of spectrum analysis. + mass spectrometry analysis - + - - - + + - - + + - - 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 - validated information + + + spread calculation data transformation + + A spread calculation is a data transformation that has objective spread calculation. + James Malone + EDITOR + spread calculation data transformation - + - - + + - - + + - curated information - PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. + Kaplan Meier - 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 - curated information + 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 - + - + - - + + - - randomized group participant role - A person enrolled in a randomized clinical trial bears a randomized group participant role + + multiple testing correction method - a role that borne by an organism and realized by some group randomization process - Person:Helen Parkinson - Philippe Rocca-Serra - randomized group participant role + 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. + multiple testing correction method - - - - - - - - - - - - - - - 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 - OBI Biomaterial - methylated polymer - - - + - + + + 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. - - - - - - - - - - - - - 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 +Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation. - an organism that is the output of a genetic transformation process - PERSON: Philippe Rocca-Serra - OBI Biomaterial - genetically modified organism + 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 - + - - + + + - - + + - - - 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 - predicted data item - - - - - - - - + + - - + + - - - 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 - mean-centered data - - - - - - - - + - - + + - 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 - edited document + 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 + 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 + Westfall and Young FWER correction + Westfall and Young family wise error rate correction - + - - - - - - - - - - - - - - - - - - - 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 - dissolved material entity + + + polynomial transformation + a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1 +variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables + + A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted. + Elisabetta Manduchi + WEB: http://mathworld.wolfram.com/Polynomial.html + polynomial transformation - + - - + + - + - extraction - nucleic acid extraction using phenol chloroform - - 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 - extraction + logarithmic transformation + + A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm. + Elisabetta Manduchi + WEB: http://en.wikipedia.org/wiki/Logarithm + logarithmic transformation - + - - + + - - - - - - - + - 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 - filtration + exponential transformation + + An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. + Elisabetta Manduchi + WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function + WEB: http://en.wikipedia.org/wiki/Exponential_function + exponential transformation - + - - - - - - - - - - - - - - - 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. + + + 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. - 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 - centrifugation + 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 - + - - + + - + - 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 - staining + 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 + SIMCA + WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies + soft independent modeling of class analogy analysis - + - - + + - - - - + + + + + + + + + + + + - - - - - - - + - 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 - washing + discriminant function analysis + + Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. + Tina Hernandez-Boussard + WEB: http://www.statsoft.com/textbook/stdiscan.html + discriminant function analysis - + - - - - - - - - + + - - - - - - - + - 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) - irradiation + canonical variate analysis + + canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form. + Tina Hernandez-Boussard + CVA + WEB: http://en.wikipedia.org/wiki/Canonical_analysis + canonical variate analysis - + - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - + - 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 - polymerization - - - - - - - - - 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 + linear discriminant functional analysis - trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity - Philippe Rocca-Serra - OBI PA - trypsination + Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective. + Tina Hernandez-Boussard + PERSON: Tina Hernandez-Boussard + linear discriminant functional analysis - + - - - - - - - - - - - - - - - - - - - - - - - - - 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 - enzymatic ligation + + + regression analysis method + + Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. + Tina Hernandez-Boussard + BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 + regression analysis method - + - - - - - - - - - - - - - - - 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 - storage + + + multiple linear regression analysis + + multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as + Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon +where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression. + Tina Hernandez-Boussard + WEB:http://en.wikipedia.org/wiki/Linear_regression + multiple linear regression analysis - + - - + + - - - - - - - - - - - + + + + + + + + + + + + - 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] - cell lysis + principal component regression + + The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. + Tina Hernandez-Boussard + WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html + principal component regression - + - - - - - - - - - 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 - electrocution + + + partial least square regression analysis + + Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that +Y = b0 + b1X1 + b2X2 + ... + bpXp +In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data. + Tina Hernandez-Boussard + PLS-RA + ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263. + partial least square regression analysis - + - - - 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 - cervical dislocation + + + discriminant analysis + + Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. + Tina Hernandez-Boussard + WEB: http://www.statsoft.com/textbook/stdiscan.html + discriminant analysis - + - - - 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 - asphyxiation + + + 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. + James Malone + PLS-DA + WEB: http://www.camo.com/rt/Resources/pls-da.html + partial least square discriminant analysis - + - - + + - - + + - 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 - lethal injection - OBI Biomaterial - intentional overdosing - - - - - - - - - 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 - decapitation - - - - - - - - - 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] - group randomization + eh transformation + This type of transformation is typically used in flow cytometry. + + An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + eh transformation - + - - - 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 - - obsolete_activation - true + + + + + + + + + + + + + + + + + b transformation + This type of transformation is typically used in flow cytometry. + + A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + b transformation - + - - + + - + - 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 - immobilization + s transformation + This type of transformation is typically used in flow cytometry. + + An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization. + Elisabetta Manduchi + Joseph Spliden + Ryan Brinkman + WEB: http://flowcyt.sourceforge.net/gating/latest.pdf + s transformation - + - - + + - + + + + + + + - - - - - - - + + + + - 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 - nucleic acid hybridization - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + 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 + visualization + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + PERSON: Tina Boussard + Possible future hierarchy might include this: +information_encoding +>data_encoding +>>image_encoding + data visualization + + + + + + + + - - + + - - + + - 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 - elution + similarity calculation + + A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + similarity calculation - + - - + + + euclidean distance calculation + + An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + euclidean distance calculation + + + + + + + + + pearson correlation coefficient calculation + + A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered. + Elisabetta Manduchi + PERSON: Elisabetta Manduchi + WEB: http://en.wikipedia.org/wiki/Correlation + pearson correlation coefficient calculation + + + + + + + + - + - DNA Subtraction - 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 + loess fitting - a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. + 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 - OBI-Branch - DNA Subtraction + ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101. + loess fitting - + - - + + - - - - + + + + + + + + + + + + - - + + - 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 + mode calculation - is a planned process with specified input original document and specified output edited document - Philippe Rocca-Serra and OBI consortium - adapted from wikipedia - document editing + A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data. + James Malone + Monnie McGee + PERSON: James Malone + PERSON: Monnie McGee + From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) + mode calculation - + - - - - - - - - + + - - + + - 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 - prediction + quantile calculation + + A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. + Monnie McGee + WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html + quantile calculation - + - - - validation - PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. + + + + + + + + + + + + + + + + + + + + + + + median calculation - 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) - validation + A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values. + James Malone + Monnie McGee + PERSON: James Malone + PERSON: Monnie McGee + From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008) + median calculation - + - - + + - - + + - - + + - electroporation - PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13. + variance calculation - 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 - electroporation + A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment. + Monnie McGee + PERSON: Monnie McGee + From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008) + variance calculation - + - - - digital curation - PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44. + + + + + + + + + + + + + + + standard deviation calculation - 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 - digital curation - - - - - - - - - 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 - - - - - - - - - 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 standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. + Monnie McGee + PERSON: Monnie McGee + From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) + standard deviation calculation - + - - + + - - + + - 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 + + + + + + + interquartile-range calculation + + The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. + Monnie McGee + PERSON: Monnie McGee + From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008) + interquartile-range calculation - + - - + + - - - - + + + + + + + + + + + + - - + + + skewness calculation + + A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment + Monnie McGee + WEB: http://www.riskglossary.com/link/skewness.htm + From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) + skewness calculation + + + + + + + + - - + + - - + + + kurtosis calculation + + A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html + Monnie McGee + WEB: http://davidmlane.com/hyperstat/A53638.html + From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008) + kurtosis calculation + + + + + + + + - - + + - 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 + data combination + + 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 + editor + data combination - + - - - 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 + + + network graph construction + + A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph. + Richard Scheuermann + PERSON: Richard Scheuermann + network graph construction - + - - - 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 + + + weighted network graph construction + + A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. + Richard Scheuermann + PERSON: Richard Scheuermann + weighted network graph construction - + - - - 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 + + + directed network graph construction + + A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph. + Richard Scheuermann + PERSON: Richard Scheuermann + directed network graph construction - + - - - 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 + + + node quality calculation + + A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network. + Richard Scheuermann + PERSON: Richard Scheuermann + node quality calculation - + - - - 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 + + + node degree calculation + + A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node. + Richard Scheuermann + PERSON: Richard Scheuermann + node degree calculation - + - - - 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 + + + quantitative node degree calculation + + A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node. + Richard Scheuermann + PERSON: Richard Scheuermann + quantitative node degree calculation - + - - - 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 + + + node in-degree calculation + + A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node. + Richard Scheuermann + PERSON: Richard Scheuermann + node in-degree calculation - + - - - 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 + + + node out-degree calculation + + A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node. + Richard Scheuermann + PERSON: Richard Scheuermann + node out-degree calculation - + - - - 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 + + + node shortest path identification + + A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network. + Richard Scheuermann + PERSON: Richard Scheuermann + node shortest path identification - + - - - 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 + + + edge quality calculation + + A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. + Richard Scheuermann + PERSON: Richard Scheuermann + edge quality calculation - + - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 + + + edge betweenness calculation + + An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge. + Richard Scheuermann + PERSON: Richard Scheuermann + edge betweenness calculation - + - - - 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 + + + network subgraph quality calculation + + A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network. + Richard Scheuermann + PERSON: Richard Scheuermann + network subgraph quality calculation - + - - - 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 + + + subgraph degree calculation + + A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + subgraph degree calculation - + - - - 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 + + + quantitative subgraph degree calculation + + A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + quantitative subgraph degree calculation - + - - - 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 + + + 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 + mathematical feature - + - - - 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 + + + + + + + + + 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 + log base - + - - - - - - - - - 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 + + + subgraph in-degree calculation + + A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + subgraph in-degree calculation - + - - - 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 + + + subgraph out-degree calculation + + A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + subgraph out-degree calculation - + - - - 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 + + + intra subgraph connectivity calculation + + A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph. + Richard Scheuermann + PERSON: Richard Scheuermann + intra subgraph connectivity calculation - + - - - 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 + + + subgraph modularity calculation + + A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. + Richard Scheuermann + PERSON: Richard Scheuermann + subgraph modularity calculation - + - - - 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 + + + network graph quality calculation + + A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole. + Richard Scheuermann + PERSON: Richard Scheuermann + network graph quality calculation - + - - + + - - + + - 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 + unit-variance scaling + + A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. + Elisabetta Manduchi + Philippe Rocca-Serra + autoscaling + PMID:16762068 + unit-variance scaling - + - - - 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 + + + 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 - + - - - 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 + + + + + + + + + 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 + exponential base - + - - - 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 + + + + + + + + + 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 + polynomial degree - + - - - 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 + + + + + + + + + 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 + number of variables - + - - - 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 + + + 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 + James Malone + bottom-up hierarchical clustering + PERSON: Elisabetta Manduchi + agglomerative hierarchical clustering - + - - - 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 + + + 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 + James Malone + top-down hierarchical clustering + PERSON: Elisabetta Manduchi + divisive hierarchical clustering - + - - - 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 + + + data partitioning + + Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. + James Malone + PERSON: Melanie Courtot + PERSON: Richard Scheuermann + PERSON: Ryan Brinkman + data partitioning - + - - - 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 + + + 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 + Richard H. Scheuermann + PERSON: Richard H. Scheuermann + data vector reduction objective - + - - - 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 + + + + + + + + + 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 + gFWER correction + 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 - + - - + + - - - - + + + + + + + + + + + + - 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 + 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 + QNFP + 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 - + - - - - - - - - - - - - - - + + - - + + - - - - - - - - - - - - - - - - - - - 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 + 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 + TPPFP correction method + 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 - + - - + + + + + + + + - - + + - - + + - 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 + 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. . + 2011-03-31: [PRS]. +creating a defined class by specifying the necessary output of dt +allows correct classification of FDR dt + 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 + false discovery rate correction method - + - - - 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 + + + + + + + + + + + + + + + + + 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 + PEFP correction method + 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 - + - - - 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 + + + + + + + + + + + + + + + + + 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 + QPFP correction method + 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 - + - - - Guava EasyCyte Plus + + + data transformation objective + normalize objective - 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 + An objective specification to transformation input data into output data + Modified definition in 2013 Philly OBI workshop + James Malone + PERSON: James Malone + data transformation objective - + - - - Guava Personal Cell Analysis + + + data normalization objective + Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. - 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 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 + James Malone + PERSON: Elisabetta Manduchi + PERSON: Helen Parkinson + PERSON: James Malone + data normalization objective - + - - - 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 + + + correction objective + Type I error correction + + 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 + correction objective - + - - - helium cadmium ion laser - KIMMON HeCd 325nm laser + + + + + + + + + + + + + + + + + normalization data transformation - 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 normalization data transformation is a data transformation that has objective normalization. + James Malone + PERSON: James Malone + normalization data transformation - + - - - helium neon ion laser - A helium neon laser can by used to irradiate cells in a flow cytometer. + + + + + + + + + + + + + + + + + averaging data transformation - 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 + An averaging data transformation is a data transformation that has objective averaging. + James Malone + PERSON: James Malone + averaging data transformation - + - - - - - - - - - + + - - + + - - 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 + + + partitioning data transformation + + A partitioning data transformation is a data transformation that has objective partitioning. + James Malone + PERSON: James Malone + partitioning data transformation - + - - - inFlux Analyzer + + + partitioning objective + A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. - 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 + 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 + James Malone + PERSON: Elisabetta Manduchi + partitioning objective - + - - - 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 + + + 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 + James Malone + PERSON: Elisabetta Manduchi + background correction objective - + - - - interrogation_point - Interrogation point in BD FACS Calibur - - Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point. - John Quinn - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11 - interrogation_point + + + 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 + James Malone + PERSON: Elisabetta Manduchi + curve fitting objective - + - - - 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 + + + + + + + + + + + + + + + + + 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 + PERSON: James Malone + class discovery data transformation - + - - - jet_in_air_flow_chamber - Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter + + + + + + + + + Fisher's exact test - A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air. - John Quinn - http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm - jet_in_air_flow_chamber + 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 - + - - - 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 + + + center calculation objective + A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average. + + 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 + center calculation objective - + - - - LactoScope C4 - LactoScope C4 Automatic Economical + + + class discovery objective - 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 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 + discriminant analysis objective + unsupervised classification objective + PERSON: Elisabetta Manduchi + PERSON: James Malone + class discovery objective - + - - - 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 + + + class prediction objective + + 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 + supervised classification objective + PERSON: Elisabetta Manduchi + PERSON: James Malone + class prediction objective - + - - - - - - - - - light source + + + spread calculation objective + Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean - 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 + 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 + spread calculation objective - + - - - 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 - - - - - - - - - long pass filter - 750 LP filter + + + + + + + + + + + + + + + + + center calculation data transformation - 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 center calculation data transformation is a data transformation that has objective of center calculation. + James Malone + PERSON: James Malone + center calculation data transformation - + - - - LSR2 - LSR2 at TSRI Flow Cytometry Core Facility + + + + + + + + + + + + + + + + + data vector reduction data transformation - 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 data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k. + James Malone + PERSON: James Malone + data vector reduction data transformation - + - - - 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 + + + scaling objective + 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 + Awaiting English definition from Monnie McGee + James Malone + Person:Helen Parkinson + scaling objective - + - - - Luminex 200 + + + + + + + + + + + + + + + + + descriptive statistical calculation data transformation - 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 descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. + James Malone + PERSON: James Malone + descriptive statistical calculation data transformation - + - - - MACS Quant + + + + + + + + + scaling data transformation - 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 scaling data transformation is a data transformation that has objective scaling. + James Malone + PERSON: James Malone + scaling data transformation - + - - - 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 + + + error correction objective + 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 + error correction objective - + - - - mixed argon-krypton gas laser - argon-krypton laser in a cytometer + + + + + + + + + sequence analysis data transformation - 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 - - - - - - - - - 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 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 + sequence analysis data transformation - + - - - multi-well plate - 96 well plate, 48 multiwell plate - - A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader. - FG this is synonymous with microtiter plate - John Quinn - http://www.nuncbrand.com/page.aspx?ID=301 - multi-well plate + + + cross validation objective + + 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 + cross validation objective - + - - - neodymium-YAG laser - Neodymium-YAG Laser in DURIP99 System + + + merging objective + merging of columns from two different data sets - 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 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 + merging objective - + - - + + - - + + + + + + + + + + + + - 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 - - - - - - - - - - + + - optical filter - 720 LP filter, 580/30 BP filter + clustered data visualization - 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 + 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 - + - - - - - - - - + + - - + + - - + + - 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 - - - - - - - - - particle delivery vessel - FC 500 particle delivery vessel + gene list visualization - Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube. - John Quinn - Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 - FG: this should be delted - particle delivery is a role that an object can play - particle delivery vessel + 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 - + - - + + - - + + + + + + + + + - 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 - - - - - - - - - photodiode - Avalanche photodiode + + + + + + + classified data visualization - 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 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 - + - - - - - - - - + + - - + + + + + + + + + - - + + - photomultiplier tube - R9647 by manufactured by Hamamatsu + background corrected data visualization - 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 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 - + - - - + + - - + + - - piezo electric crystal - quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar + + + survival analysis data transformation - 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 - piezo electric crystal + A data transformation which has the objective of performing survival analysis. + James Malone + PERSON: James Malone + survival analysis data transformation - + - - + + - - + + - plate loader - FC 500 plate loader + proportional hazards model estimation - 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 + 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 - + - - - preamplifier - Built in preamplifier in a Hamamatsu H9656 PMT + + + correlation study objective - 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 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 - + - - - quartz cuvette flow chamber - CVF-Q-10 flow chamber, CV-Q-10 flow chamber + + + spectrum analysis objective + Calculation of characteristic path length in mass spectrometry - 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 + 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 - + - - - 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 + + + + + + + + + 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 - + - - - cytometer sample tube - sample tube in a cytometer + + + + + + + + + gas chromatography mass spectrometry - 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 + 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 - + - - - - - - - - + + - - + + - sheath tank - LSR2 sheath tank + chi square test - 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 + 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 - + - - - short pass filter - 620 SP filter + + + ANOVA - 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 + 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 - + - - - 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 + + + 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 - + - - - Somacount + + + 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 + + + + + + + + + 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) + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pool of specimens + + 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 + pool of specimens + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + chemical solution + 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 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 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 + liquid chemical solution + GROUP: OBI Biomaterial Branch + chemical solution - + - - - 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 + + + 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 + buffer 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) + solvent role + + + + + + + + - - + + - - + + - 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 + 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) + solute role - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - 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 - - - - - - - - - - + + - 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 - - - - - - - - - - + + + + + + + - 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 + 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 - + - - + + - - + + - 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 - - - - - - - - - - + + - - + + - 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 + + + + + + + + + + + + + + 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 - + - - + + + 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 + + obsolete_liver + true + + + + + + + + + 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 + + obsolete_adipose tissue + true + + + + + + + + + + + + + + + + + + + denatured polymer + + Is a polymer which has lost secondary or tertiary structure + PERSON: Alan Ruttenberg + http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 + denatured polymer + + + + + + + + + + + + + + + + + + + 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 + OBI Biomaterial + decapitated organism + + + + + + + + - - + + - arrayer - BioRobotics Microgrid II TAS, Affymetrix GMS 417 + validated information + PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." - A device which deposits biological material onto a substrate in a defined pattern. - Trish Whetzel - MO_697 arrayer - arrayer + 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 + validated information - + - - + + - - - - - - - + + - + 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 + curated information + + + + + + + + - - + + - - + + + 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 + randomized group participant role + + + + + + + + + + + + + + + + + + + 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 + OBI Biomaterial + methylated polymer + + + + + + + + + + + + + + + + + + + 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 + OBI Biomaterial + genetically modified organism + + + + + + + + - - - - - - - - - - - - + + - - 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 + + + 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 + predicted data item - + - - - + + - - + + - - 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 + + + 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 + mean-centered data - + - - + + - - + + - heating block - An instrument used to heat and/or maintain material at a set temperature. + edited document + The OBI manuscript is (much) edited imformation - 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 document which is the output of a document editing process + Person:Bjoern Peters + Philippe Rocca-Serra + edited document - + - - + + + + + + + + + + + + + + + + + + + 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 + dissolved material entity + + + + + + + + - - + + - 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 + extraction + nucleic acid extraction using phenol chloroform + + 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 + extraction - + - - + + - - + + - - + + - hybridization chamber - Glass Array Hybridization Cassette + filtration + PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4. - 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 + 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 + filtration - + - - + + - - + + - - + + - hybridization station - Labnet Problot12 + 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. - 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 + 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 + centrifugation - + - - + + - - + + - 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 + 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 + staining - + - - + + - - + + - - + + - oligonucleotide synthesizer - Automated Multiplex Oligonucleotide Synthesizer - - An instrument used to chemically synthesize oligonucleotides. - Trish Whetzel - MO - oligonucleotide synthesizer - - - - - - - - - - + + - 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 + 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 + washing - + - - + + - - + + - 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 + + + + + + + + + + + + + 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) + irradiation - + - - + + - - + + - - + + - 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 + + + + + + + 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 + polymerization - + - - - - - - - - + + + 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 + trypsination + + + + + + + + - - + + + + + + + + + + + + - - + + - vacuum dryer - Model 777 Microarray Oven + 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 instrument which removes liquid by the application of negative pressure, i.e. vacuum. - Trish Whetzel - MO - vacuum dryer + 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 + enzymatic ligation - + - - + + - - + + - 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 + + + + + + + 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 + storage - + - - + + - - + + + + + + + + + - microarray wash station - ArrayIt(r) Microarray Wash Station + 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. - A device that is used to wash Affymetrix-type arrays. - Trish Whetzel - MO_626 wash_station - microarray wash station + 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] + cell lysis - + - - + + - - + + + 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 + electrocution + + + + + + + + + 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 + cervical dislocation + + + + + + + + + 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 + asphyxiation + + + + + + + + - - + + - 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. + 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 - 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 + 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 + lethal injection + OBI Biomaterial + intentional overdosing - + - - + + + 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 + decapitation + + + + + + + + + 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] + group randomization + + + + + + + + + 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 + + obsolete_activation + true + + + + + + + + - - + + + 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 + immobilization + + + + + + + + - - + + + + + + + + + + + + - 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 + 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 + nucleic acid hybridization - + - - + + - - + + + + + + + + + + + + - - + + - - + + - - + + - 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 + 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 + elution - + - - - - - - - - + + - - + + + DNA Subtraction + 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 + DNA Subtraction + + + + + + + + - - + + - - + + - cytometer - - A cytometer is an instrument for counting and measuring cells. - Melanie Courtot - http://medical.merriam-webster.com/medical/cytometer - cytometer + 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 + document editing - + - - + + - - + + - - + + - 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 + 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 + prediction - + - - - - - - - - - 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 - - - - - - - - - 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 + + + 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) + validation - + - - - - - - - - + + - - + + - - + + - 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 + 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 + electroporation - + - - - 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 + + + 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 + digital curation - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - + - + - droplet sorter + analog-to-digital converter + The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection. - 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 - - - - - - - - - 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 - - - - - - - - - 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 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 - + - - + + - - + + - 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 - - - - - - - - - - + + - - + + - 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 - - - - - - - - - - + + - + - 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 + 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 + + + + + + + + + arc lamp + The Jablochkoff Candle - 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 + 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 - + - - - - - - - - - microscope slide - PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. + + + argon ion laser + argon ion laser in a cytometer - 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 + 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 - + - - - - - - - - - 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 + + + 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 - + - - - - - - - - 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. + + + Bactiflow - 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 + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + + + + + + + + + + + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + + + + + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + 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 - + - - - 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 + + + + + + + + + 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 - + - - - 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 + + + 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 - + - - - stopping rule - PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy. - - a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen - PRS - PRS - stopping rule + + + 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 - + - - - compliance rule - - a compliance rule is a rule which ensures a compliance process occurs - PRS - PRS - compliance rule + + + 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 - + - - - standard compliance rule - - a standard compliance rule is a compliance rule which defines conformity to a representation standard - PRS - PRS - standard compliance rule + + + 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 - + - - - ethical standard compliance rule - - an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur - PRS - PRS - ethical standard compliance rule + + + 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 - + - - - eligibility criterion - PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. + + + FACS Scan - an eligibility criterion (rule) is_a selection criterion which -defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. - - Person: Philippe Rocca-Serra - eligibility rule - Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group - eligibility criterion + 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 - + - - - inclusion criterion - PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) . - - an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. - Person: Philippe Rocca-Serra - inclusion condition - inclusion rule - Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group - inclusion criterion + + + 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 - + - - - exclusion rule - PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. - - an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study - Person: Philippe Rocca-Serra - Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group - exclusion criterion + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + + 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 + + + + + + + + - - + + + 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 + + + + + + + + - - + + - - + + - adding substance to cell culture - 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 - Bjoern Peters - IEDB - adding substance to cell culture - - - - - - - - - - + + - - - - - - - + + - - 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 + + + + + + + + + + + + + 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 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 - performing a clinical assessment + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - human subject enrollment - 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 - Bjoern Peters - IEDB - criteria come from plan / clinical trial branch - human subject enrollment + + + 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 - + - - - - - - - - - - - - - - - - - - - - - collecting specimen from organism - taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient + + + Guava EasyCyte Mini - a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation - PERSON:Bjoern Peters - IEDB - collecting specimen from organism + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - killing - Terminal sacrifice of animals by cervical dislocation at the end of an investigation. - - 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 - death status type - euthanisia - life termination - sacrifice - CEBS, Biomaterial_branch - killing + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - administering substance in vivo - 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 - 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 - IEDB - administering substance in vivo + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - acquisition - Downloading a 3D structure from the PDB. Purchasing antibodies from sigma. + + + Guava Personal Cell Analysis-96 - the planned process of gaining possession of a continuant - 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' - Bjoern Peters - IEDB - This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition - acquisition + 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 - + - - - exposure of material to environment - Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. + + + helium cadmium ion laser + KIMMON HeCd 325nm laser - a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. - Bjoern Peters - IEDB - Alan says there will be problmes, e.g. with selection by survival - exposure of material to environment - - - - - - - - - - - - - - - material acquisition - 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 - This excludes processes that create or change materials, such as material transformations. - Bjoern Peters, Alan Ruttenberg, Helen Parkinson - material procurement - IEDB - material acquisition + 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 - + - - - acclimatization - placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress - - A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. - Jennifer Fostel - CEBS, Biomaterial_branch - acclimatization + + + 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 - + - - - - - - - - + + - - + + - - + + - environmental material collection - Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas - - environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer. - relabel the term and add axiom connecting to EnVO:'environmental material' -discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/ - Bjoern Peters, Alan Ruttenberg - IEDB - the researcher is very interested in the location - environmental material collection process + 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 - + - - - - - - - - - information acquisition - Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC + + + inFlux Analyzer - 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 - OBI branch derived - information acquisition + 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 - + - - - - - - - - - - - - - - - - - - - - - material component separation - Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification + + + Influx Cell Sorter + Influx Cell Sorter at TSRI Flow Cytometry Core Facility - a material processing in which components of an input material become segregated in space - Bjoern Peters - IEDB - material component separation + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - group assignment - Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation + + + interrogation_point + Interrogation point in BD FACS Calibur + + Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point. + John Quinn + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11 + interrogation_point + + + + + + + + + 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 + + + + + + + + + jet_in_air_flow_chamber + Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter + + A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air. + John Quinn + http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm + jet_in_air_flow_chamber + + + + + + + + + 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 + + + + + + + + + LactoScope C4 + LactoScope C4 Automatic Economical - 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 - OBI Plan - group assignment + 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 - + - - - - - - - - + + + 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 + + + + + + + + - - + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + multi-well plate + 96 well plate, 48 multiwell plate + + A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader. + FG this is synonymous with microtiter plate + John Quinn + http://www.nuncbrand.com/page.aspx?ID=301 + multi-well plate + + + + + + + + + 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 + + + + + + + + - - + + + 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 + + + + + + + + - - 2 + + - 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 - PlanAndPlannedProcess Branch - sample pooling - OBI branch derived - like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. - pooling specimens + 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 - + - - + + - - + + - - + + - - - - - - - + + - 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 + 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 - + - - + + + particle delivery vessel + FC 500 particle delivery vessel + + Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube. + John Quinn + Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 + FG: this should be delted - particle delivery is a role that an object can play + particle delivery vessel + + + + + + + + - - + + - material portioning - pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock + photodetector + A photomultiplier tube, a photo diode - a material processing in which the input substance is partitioned into a number of portions that are similar in composition. - PERSON:Bjoern Peters - aliquoting - apportioning - OBI branch derived - material portioning + 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 - + - - - non-specific labeling - The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. - - The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial - PlanAndPlannedProcess Branch - OBI branch derived - definition blessed by Allyson, Bjoern, Jay & Randi - non-specific labeling + + + 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 - + - - + + - - + + - - + + - - - - - - - - - - - - - - + + - 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 + 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 - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + 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 + piezo electric crystal + + + + + + + + - - + + - cell fixation - http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus - - a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time - should include capturing what qualities are being preserved - PERSON:Bjoern Peters - OBI branch derived - we could generalize this for other input materials - cell fixation + 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 - + - - + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + - - + + - excision - Cutting out the portion of a gel which contains a DNA fragment - - the use physical means to remove a portion of a substance from the rest - Alan Ruttenberg, Kevin Clancy - www.crohnsresource.com/glossary.jsp (via google define:resection) - excision + + + + + + + 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 - + - - - - non specific enzymatic cleavage - The use of agarase to digest an agar gel - - an enzymatic cleavage that uses an enzyme without a strong affinity for specific cleavage sites in the input material - PERSON:Kevin Clancy - OBI branch derived - non specific enzymatic cleavage + + + 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 - + - - + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + - - + + - - - - - - - - - + + - - + + - - + + - maintaining cell culture - When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture - - a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing - PlanAndPlannedProcess Branch - OBI branch derived - maintaining cell culture + + + + + + + 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 - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - + + - the detection of phycoerytherin by means of flow cytometry - - An assay that detects a specified substance - Kevin Clancy - OBI branch derived - substance detection assay + 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 - + - - + + - - + + + 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 + + + + + + + + - - + + - 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 + 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 - + - - + + - - + + - artificially induced cell membrane lysis - http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent. - - a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate - ---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined. - PlanAndPlannedProcess Branch - OBI branch derived - artificially induced cell membrane lysis + 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 - + - - + + - - + + - - + + + 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 + + + + + + + + - - + + + 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 + + + + + + + + - - + + + + + + + - artificially induced reverse transcription - 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. - 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 - artificially induced reverse transcription + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + - - + + - isolation of cell culture supernatant - Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube. - - a protocol which results in the separation of supernatant material from a cell culture - This does not apply to the case where the cells are lysed - PlanAndPlannedProcess Branch - OBI branch derived - isolation of cell culture supernatant + 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 - + - - + + - - + + - experimental disease induction - the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome. - - a protocol application to induce a specific disease in an organism - PlanAndPlannedProcess Branch - OBI branch derived - could be defined class - experimental disease induction + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - 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 + 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 - + - - + + - - + + - artificially induced DNA repair - the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands - - a protocol application to repair damaged DNA molecules - PlanAndPlannedProcess Branch - OBI branch derived - ---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi - artificially induced DNA repair + + + + + + + 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 - + - - - - - - - - + + - - + + - - + + - cell permeabilization - Electroporation of HeLa cells to allow transfection with pUC19. + hybridization station + Labnet Problot12 - A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application - need to add output cell has_quality permeable - PERSON:Bjoern Peters - OBI branch derived - definition blessed by Jay, Alan, Randi - cell permeabilization + 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 - + - - + + - - + + - precipitation - The use of ethanol to precipitate DNA molecules from a solution containing DNA - - a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate) - PERSON:Kevin Clancy - OBI branch derived - precipitation + 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 - + - - - - - - - - + + - - + + - - + + + oligonucleotide synthesizer + Automated Multiplex Oligonucleotide Synthesizer + + An instrument used to chemically synthesize oligonucleotides. + Trish Whetzel + MO + oligonucleotide synthesizer + + + + + + + + - - + + - 'establishing cell culture' - - a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). - PERSON:Matthew Brush - PERSON:Matthew Brush - A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. - establishing cell culture + 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 - + - - + + - - + + + 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 + + + + + + + + - - + + - - + + - cell culture splitting - The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. - - 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 - 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 + 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 - + - - + + - - + + - - + + - - + + + 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 + + + + + + + + - - + + - addition of molecular label - The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. - - 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 - OBI developer call, 3-12-12 - addition of molecular label + 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 - + - - + + - - + + - artificially induced methylation - the use of enzymes to add methyl groups to DNA molecules + microarray wash station + ArrayIt(r) Microarray Wash Station - A planned process of adding methyl groups to polymers - PERSON:Kevin Clancy - OBI branch derived - artificially induced methylation + A device that is used to wash Affymetrix-type arrays. + Trish Whetzel + MO_626 wash_station + microarray wash station - + - - - - - - - - + + - - + + - - + + - synthesis - making cDNA from nucleotides using RNA as a template - - the construction of a biomaterial from simpler biomaterials - This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription - PERSON:Kevin Clancy - synthesize - OBI branch derived - synthesis + 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 - + - - + + - - + + - concentrate - Evaporation of the solution containing DNA to increase the concentration of the DNA molecules - - a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material - PERSON:Kevin Clancy - OBI branch derived - concentrate - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - recombinant plasmid cloning - The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35. - - the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial - PERSON:Kevin Clancy - OBI branch derived - recombinant plasmid cloning + + + + + + + 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 - + - - + + - - + + - - + + - genetic transformation - The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 - - the introduction. alteration or integration of genetic material into a cell or organism - PERSON:Kevin Clancy - genetic modification - OBI branch derived - genetic transformation - - - - - - - - - - + + - lavage - the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present - - A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid - This is not washing, in which case the material of interest is not the resulting fluid - PlanAndPlannedProcess Branch - OBI branch derived - lavage - - - - - - - - - - - - - - - - - - - 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 + + + + + + + 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 - + - - + + - - + + - - + + - - + + - - + + - preparative chromatography - The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides. - - the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity - PERSON:Kevin Clancy; Bjoern Peters - OBI branch derived - preparative chromatography - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - PERSON:Kevin Clancy - OBI branch derived - vector mediated amplification + cytometer + + A cytometer is an instrument for counting and/or measuring characteristics of cells. + Melanie Courtot + http://medical.merriam-webster.com/medical/cytometer + cytometer - + - - + + - - + + - - - - - - - - - - - - + + - DNA polymerase amplification - The use of taq polymerase to amplify a DNA fragment during a PCR. - - 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 - OBI branch derived - DNA polymerase amplification - - - - - - - - - specific enzymatic cleavage - The use of a protease to digest a protein into peptides - - an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material - PERSON:Kevin Clancy - OBI branch derived - specific enzymatic cleavage + 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 - + - - + + - - + + - gradient separation - the use of a sucrose gradient to isolate mitochondria + power supply + A AC/DC transformer that generates the reqired power for an electrophoresis apparatus - a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities - PERSON:Kevin Clancy - OBI branch derived - gradient separation + 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 - + - - - - - - - - - dialysis - the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage - - a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition - PERSON:Kevin Clancy - OBI branch derived - dialysis + + + 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 - + - - - - - - - - - - - - - - - + + - - + + - - + + - - + + - electrophoresis - Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change. - - a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge - PERSON:Kevin Clancy - OBI branch derived - Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers. - electrophoresis + 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 - + - - - - - - - - - selection by survival - The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected - - the use of environmental conditions to select for the organism or cells that have a certain trait - PERSON:Kevin Clancy - OBI branch derived - selection by survival + + + 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 - + - - - - - - - - - DNA cleavage, restriction analysis - the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components + + + 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 + + + + + + + + + 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 specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence - PERSON:Kevin Clancy - restriction enzyme assay - DNA restriction enzyme digestion + 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 - + - - - - - - - - - - - - - - - - - - + + - - + + - protease cleavage - the use of trypsin to cleave pepsin into peptide fragments - - protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). - enzymatic digestion - PlanAndPlannedProcess Branch - OBI branch derived - protease cleavage + 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 - + - - - enzymatic DNA replication - the use of enzymes to duplicate DNA molecules - - the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial - PERSON:Kevin Clancy - OBI branch derived - enzymatic DNA replication + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - enzymatic amplification - the use of a polymerase chain reaction to amplify a fragment of DNA - - the use of enzymes to increase the number of molecules of a biomaterial - PERSON:Kevin Clancy - OBI branch derived - enzymatic amplification + + + 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 - + - - + + - - + + - DNA transduction - The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein - - a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism - PERSON:Kevin Clancy - OBI branch derived - DNA transduction + 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 - + - - + + - - - - - - - - - - - - + + - DNA transfection - The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest + + + + + + + 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 transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell - PERSON:Kevin Clancy - OBI branch derived - DNA transfection - - - - - - - - - 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. - - 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 - PlanAndPlannedProcess Branch - OBI branch derived - vector mediated expression + 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 - + - - + + - - + + - - + + + 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 + + + + + + + + - - - - - - - - - - - - + + + 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 + + + + + + + + - - + + + 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 + + + + + + + - - + + - recombinant vector cloning - - 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 - OBI branch derived - recombinant vector cloning + 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 + experimental design + rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. + study design - + - - - - Place holder class, see editor note + + + 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 - OBI branch derived - - obsolete_defined processes - true + Clinical Research Glossary Version 4.0 CDICS glossary group + clinical study design - + - - - specific labeling - The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells + + + 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 labeling in which the labeling reagent used has a specificity to bind only certain components of the input material - PlanAndPlannedProcess Branch - OBI branch derived - definition blessed by Allyson, Bjoern, Jay & Randi - specific labeling + 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 - + - - - - - - - - - RNA extraction - - A RNA extraction is a nucleic acid extraction where the desired output material is RNA - PlanAndPlannedProcess Branch - OBI branch derived - requested by Helen Parkinson for MO - RNA extraction + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - - nucleic acid extraction - Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. + + + n-to-1 design - a material separation to recover the nucleic acid fraction of an input material - PlanAndPlannedProcess Branch - OBI branch derived - requested by Helen Parkinson for MO. Could be defined class - nucleic acid extraction + 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 - + - - - - - - - - - - - - - - - cell culture supernatant - solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. -Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615 - - Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell. - PERSON: Bjoern Peters - GROUP: IEDB - cell culture supernatant + + + 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 - + - - - - - - - - - - - - - - - - - - - - - - cell pellet - Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214 - - 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 - GROUP: CEBS - GROUP: OBI Biomaterial Branch - cell pellet + + + 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 - + - - - - - - - - - - - - - - - phage display library - PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] - - a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. - PERSON: Bjoern Peters - PERSON: Philippe Rocca-Serra - display library - WEB: http://www.immuneepitope.org/home.do - PRS: 22022008. class moved under population, -modification of definition and replacement of biomaterials in previous definition with 'material' -addition of has_role restriction - phage display library + + + 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 - + - - - - - - - - - - - - - - - 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 - - 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 - GROUP: PSI - cell lysate + + + 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 - - - - - - - - - - - - - - - - - peptide construct - Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin + -A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617 - - a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion - PERSON: Bjoern Peters - IEDB - peptide construct + + + 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 - + - - - - - - - - - transgenic organism - HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein -Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162 - - 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 - GROUP:IEDB - transgenic organism + + + 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 - + - - - - - - - - - - - - - - - whole mount tissue + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 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 - whole mount sample - GROUP: OBI - PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity - PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application - whole mount tissue + 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 - + - - - assay bead - Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. - - A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. - DS: Probably better modeled as a role. - OBI - bead - assay bead + + + 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 - + - - - - - - - - - epitope + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 material entity bearing the epitope role - IEDB - IEDB - epitope + 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 - + - - - - An occurrence of disease is a process involving pathologic changes within an organism - IEDB - IEDB - - obsolete_occurrence of disease - true + + + 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 - + - + + + stopping rule + PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy. + + a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen + PRS + PRS + stopping rule + + + + + + + + + compliance rule + + a compliance rule is a rule which ensures a compliance process occurs + PRS + PRS + compliance rule + + + + + + + + + standard compliance rule + + a standard compliance rule is a compliance rule which defines conformity to a representation standard + PRS + PRS + standard compliance rule + + + + + + + + + ethical standard compliance rule + + an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur + PRS + PRS + ethical standard compliance rule + + + + + + + + + eligibility criterion + PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. + + an eligibility criterion (rule) is_a selection criterion which +defines and states the requirements (positive or negative) for an entity to be considered as suitable for a given task or participation in a process. + + Person: Philippe Rocca-Serra + eligibility rule + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group + eligibility criterion + + + + + + + + + inclusion criterion + PMID: 23979341-The major inclusion criterion was patients in whom severe cerebral embolism was diagnosed at age 75 or younger (more than 9 in the NIHSS score on day 7 after the onset of stroke) . + + an inclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity suitable for a given task or participation in a given process. For instance, in a study protocol, inclusion criteria indicate the conditions that prospective subjects MUST meet to be eligible for participation in a study. + Person: Philippe Rocca-Serra + inclusion condition + inclusion rule + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group + inclusion criterion + + + + + + + + + exclusion rule + PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. + + an exclusion criterion (rule) is_a *eligibility criterion* which defines and states a condition which, if met, makes an entity unsuitable for a given task or participation in a given process. For instance, in a study protocol, exclusion criteria indicate the conditions that prospective subjects SHOULD NOT meet to be eligible for participation in a study + Person: Philippe Rocca-Serra + Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group + exclusion criterion + + + + + + + - - - - - - - - - - - - + + - + - + - - + + @@ -75468,67 +75332,88 @@ Possible ecological risks of transgenic organism release when transgenes affect - - host exposure to infectious agent - - a process in which an infectious agent comes into physical contact with a host organism. - IEDB + + + + + + + + + + + + + + + + + + + + adding substance to cell culture + 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 + Bjoern Peters IEDB - host exposure to infectious agent + adding substance to cell culture - + - - + + - + + + + + + + - - - - - - - - - + + + + - administration in vivo with infectious agent - - is an administration of an infectious agent to a host organism - IEDB - IEDB - administration in vivo with infectious agent + + 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 - + - - + + + - - + + - - + - + - + - - + + @@ -75537,608 +75422,27916 @@ Possible ecological risks of transgenic organism release when transgenes affect - - + + - occurrence of infectious disease - - Is an occurrence of a disease caused by an infection - IEDB - IEDB - occurrence of infectious disease + + 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 + performing a clinical assessment - + - - + + - - + + - 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 - IEDB - disposition to cause an 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 - IEDB - allergic reaction - - - - - - - - - - - - - - - - - - - occurrence of allergy - - The process of an allergic disease occurring in an organism. - IEDB + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + human subject enrollment + 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 + Bjoern Peters IEDB - occurrence of allergy + criteria come from plan / clinical trial branch + human subject enrollment - + - - - - - - - - - - - - - An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-2 production by T cells + + + + + + + + + + + + + + + + + + + + + collecting specimen from organism + taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient + + a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation + PERSON:Bjoern Peters + IEDB + collecting specimen from organism - + - - + + + - + - + - - - - - - - - - - - - + + - - - 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 - IEDB - epitope binding by adaptive immune receptor + + + + + + + + + + + + + + + + + + + + + + + + killing + Terminal sacrifice of animals by cervical dislocation at the end of an investigation. + + 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 + death status type + euthanisia + life termination + sacrifice + CEBS, Biomaterial_branch + killing - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - Immunization in vivo - - Process of administering an object playing the role of immunogen to a living organism - IEDB + + + + + + + + + + + + + + + + 1 + + + administering substance in vivo + 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 + 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 IEDB - Immunization in vivo + administering substance in vivo - + - - + + - + - - - - - - - + + + + - - + + + + + + + + + - 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 + acquisition + 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. + 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' + Bjoern Peters IEDB - adaptive immune effector function + This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition + acquisition - + - - - 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 - IEDB + + + exposure of material to environment + Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. + + a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input. + Bjoern Peters IEDB - living with infected household contact + Alan says there will be problmes, e.g. with selection by survival + exposure of material to environment - + - - - 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 - IEDB + + + + + + + + + material acquisition + 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 + This excludes processes that create or change materials, such as material transformations. + Bjoern Peters, Alan Ruttenberg, Helen Parkinson + material procurement IEDB - living in endemic area + material acquisition - + - - - 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 - IEDB - IEDB - pathogen release in laboratory accident + + + acclimatization + placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress + + A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment. + Jennifer Fostel + CEBS, Biomaterial_branch + acclimatization - + - - - - - - - - + + - + - + - + - Immunization in vitro + environmental material collection + Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas - Process of administering an object playing the role of immunogen to a cell culture - IEDB + environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer. + relabel the term and add axiom connecting to EnVO:'environmental material' +discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/ + Bjoern Peters, Alan Ruttenberg IEDB - Immunization in vitro + the researcher is very interested in the location + environmental material collection process - + - - - - - - - - + + - - + + - infection process - - the detrimental process in which an infectious agent colonizes or replicates in a host environment - IEDB - IEDB - infection process + information acquisition + Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC + + 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 + OBI branch derived + information acquisition - + - + - - - - - - - + + + + - - adaptive immune receptor - - is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. - IEDB + + + + + + + + + + + + + + material component separation + Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification + + a material processing in which components of an input material become segregated in space + Bjoern Peters IEDB - adaptive immune receptor + material component separation - + - - + + + - - + + - - - immunogen - - a material entity bearing the immunogen role - IEDB - IEDB - immunogen + + + + + + + + + + + + + + + + + + group assignment + Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation + + 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 + OBI Plan + group assignment - + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + 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 + PlanAndPlannedProcess Branch + sample pooling + OBI branch derived + like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class. + pooling specimens + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + material portioning + pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock + + a material processing in which the input substance is partitioned into a number of portions that are similar in composition. + PERSON:Bjoern Peters + aliquoting + apportioning + OBI branch derived + material portioning + + + + + + + + + non-specific labeling + The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. + + The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial + PlanAndPlannedProcess Branch + OBI branch derived + definition blessed by Allyson, Bjoern, Jay & Randi + non-specific labeling + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell fixation + http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus + + a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time + should include capturing what qualities are being preserved + PERSON:Bjoern Peters + OBI branch derived + we could generalize this for other input materials + cell fixation + + + + + + + + + + + + + + + excision + Cutting out the portion of a gel which contains a DNA fragment + + the use physical means to remove a portion of a substance from the rest + Alan Ruttenberg, Kevin Clancy + www.crohnsresource.com/glossary.jsp (via google define:resection) + excision + + + + + + + + + + non specific enzymatic cleavage + The use of agarase to digest an agar gel + + an enzymatic cleavage that uses an enzyme without a strong affinity for specific cleavage sites in the input material + PERSON:Kevin Clancy + OBI branch derived + non specific enzymatic cleavage + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + maintaining cell culture + When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture + + a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing + PlanAndPlannedProcess Branch + OBI branch derived + maintaining cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + the detection of phycoerytherin by means of flow cytometry + + An assay that detects a specified substance + Kevin Clancy + OBI branch derived + substance detection 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 + + + + + + + + + + + + + + + artificially induced cell membrane lysis + http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&amp;list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent. + + a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate + ---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined. + PlanAndPlannedProcess Branch + OBI branch derived + artificially induced cell membrane lysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + artificially induced reverse transcription + 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. + 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 + artificially induced reverse transcription + + + + + + + + + + + + + + + isolation of cell culture supernatant + Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube. + + a protocol which results in the separation of supernatant material from a cell culture + This does not apply to the case where the cells are lysed + PlanAndPlannedProcess Branch + OBI branch derived + isolation of cell culture supernatant + + + + + + + + + + + + + + + experimental disease induction + the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome. + + a protocol application to induce a specific disease in an organism + PlanAndPlannedProcess Branch + OBI branch derived + could be defined class + experimental disease induction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + artificially induced DNA repair + the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands + + a protocol application to repair damaged DNA molecules + PlanAndPlannedProcess Branch + OBI branch derived + ---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi + artificially induced DNA repair + + + + + + + + + + + + + + + + + + + + + + + + + + + cell permeabilization + Electroporation of HeLa cells to allow transfection with pUC19. + + A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application + need to add output cell has_quality permeable + PERSON:Bjoern Peters + OBI branch derived + definition blessed by Jay, Alan, Randi + cell permeabilization + + + + + + + + + + + + + + + precipitation + The use of ethanol to precipitate DNA molecules from a solution containing DNA + + a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate) + PERSON:Kevin Clancy + OBI branch derived + precipitation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'establishing cell culture' + + a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). + PERSON:Matthew Brush + PERSON:Matthew Brush + A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. + establishing cell culture + + + + + + + + + + + + + + + + + + + + + + + + + + + cell culture splitting + The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media. + + 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 + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + addition of molecular label + The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+. + + 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 + OBI developer call, 3-12-12 + addition of molecular label + + + + + + + + + + + + + + + artificially induced methylation + the use of enzymes to add methyl groups to DNA molecules + + A planned process of adding methyl groups to polymers + PERSON:Kevin Clancy + OBI branch derived + artificially induced methylation + + + + + + + + + + + + + + + + + + + + + + + + + + + synthesis + making cDNA from nucleotides using RNA as a template + + the construction of a biomaterial from simpler biomaterials + This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription + PERSON:Kevin Clancy + synthesize + OBI branch derived + synthesis + + + + + + + + + + + + + + + concentrate + Evaporation of the solution containing DNA to increase the concentration of the DNA molecules + + a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material + PERSON:Kevin Clancy + OBI branch derived + concentrate + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + recombinant plasmid cloning + The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35. + + the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial + PERSON:Kevin Clancy + OBI branch derived + recombinant plasmid cloning + + + + + + + + + + + + + + + + + + + + + genetic transformation + The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 + + the introduction. alteration or integration of genetic material into a cell or organism + PERSON:Kevin Clancy + genetic modification + OBI branch derived + genetic transformation + + + + + + + + + + + + + + + lavage + the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present + + A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid + This is not washing, in which case the material of interest is not the resulting fluid + PlanAndPlannedProcess Branch + OBI branch derived + lavage + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + preparative chromatography + The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides. + + the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity + PERSON:Kevin Clancy; Bjoern Peters + OBI branch derived + preparative chromatography + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + PERSON:Kevin Clancy + OBI branch derived + vector mediated amplification + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + DNA polymerase amplification + The use of taq polymerase to amplify a DNA fragment during a PCR. + + 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 + OBI branch derived + DNA polymerase amplification + + + + + + + + + specific enzymatic cleavage + The use of a protease to digest a protein into peptides + + an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material + PERSON:Kevin Clancy + OBI branch derived + specific enzymatic cleavage + + + + + + + + + + + + + + + gradient separation + the use of a sucrose gradient to isolate mitochondria + + a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities + PERSON:Kevin Clancy + OBI branch derived + gradient separation + + + + + + + + + + + + + + + dialysis + the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage + + a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition + PERSON:Kevin Clancy + OBI branch derived + dialysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + electrophoresis + Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change. + + a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge + PERSON:Kevin Clancy + OBI branch derived + Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers. + electrophoresis + + + + + + + + + + + + + + + selection by survival + The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected + + the use of environmental conditions to select for the organism or cells that have a certain trait + PERSON:Kevin Clancy + OBI branch derived + selection by survival + + + + + + + + + + + + + + + DNA cleavage, restriction analysis + the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components + + A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence + PERSON:Kevin Clancy + restriction enzyme assay + DNA restriction enzyme digestion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + protease cleavage + the use of trypsin to cleave pepsin into peptide fragments + + protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). + enzymatic digestion + PlanAndPlannedProcess Branch + OBI branch derived + protease cleavage + + + + + + + + + enzymatic DNA replication + the use of enzymes to duplicate DNA molecules + + the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial + PERSON:Kevin Clancy + OBI branch derived + enzymatic DNA replication + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + enzymatic amplification + the use of a polymerase chain reaction to amplify a fragment of DNA + + the use of enzymes to increase the number of molecules of a biomaterial + PERSON:Kevin Clancy + OBI branch derived + enzymatic amplification + + + + + + + + + + + + + + + DNA transduction + The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein + + a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism + PERSON:Kevin Clancy + OBI branch derived + DNA transduction + + + + + + + + + + + + + + + + + + + + + + + + + DNA transfection + The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest + + a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell + PERSON:Kevin Clancy + OBI branch derived + DNA transfection + + + + + + + + + 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. + + 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 + PlanAndPlannedProcess Branch + OBI branch derived + vector mediated expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + recombinant vector cloning + + 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 + OBI branch derived + recombinant vector cloning + + + + + + + + + + Place holder class, see editor note + PlanAndPlannedProcess Branch + OBI branch derived + + obsolete_defined processes + true + + + + + + + + + specific labeling + The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells + + a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material + PlanAndPlannedProcess Branch + OBI branch derived + definition blessed by Allyson, Bjoern, Jay & Randi + specific labeling + + + + + + + + + + + + + + + RNA extraction + + A RNA extraction is a nucleic acid extraction where the desired output material is RNA + PlanAndPlannedProcess Branch + OBI branch derived + requested by Helen Parkinson for MO + RNA extraction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nucleic acid extraction + Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. + + a material separation to recover the nucleic acid fraction of an input material + PlanAndPlannedProcess Branch + OBI branch derived + requested by Helen Parkinson for MO. Could be defined class + nucleic acid extraction + + + + + + + + + + + + + + + + + + + + + cell culture supernatant + solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1. +Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615 + + Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell. + PERSON: Bjoern Peters + GROUP: IEDB + cell culture supernatant + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell pellet + Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214 + + 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 + GROUP: CEBS + GROUP: OBI Biomaterial Branch + cell pellet + + + + + + + + + + + + + + + + + + + + + phage display library + PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides] + + a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified. + PERSON: Bjoern Peters + PERSON: Philippe Rocca-Serra + display library + WEB: http://www.immuneepitope.org/home.do + PRS: 22022008. class moved under population, +modification of definition and replacement of biomaterials in previous definition with 'material' +addition of has_role restriction + phage display library + + + + + + + + + + + + + + + + + + + + + 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 + + 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 + GROUP: PSI + cell lysate + + + + + + + + + + + + + + + + + + + + + peptide construct + Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin + +A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617 + + a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion + PERSON: Bjoern Peters + IEDB + peptide construct + + + + + + + + + + + + + + + transgenic organism + HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein +Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162 + + 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 + GROUP:IEDB + transgenic organism + + + + + + + + + + + + + + + + + + + + + whole mount tissue + + 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 + whole mount sample + GROUP: OBI + PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity + PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application + whole mount tissue + + + + + + + + + assay bead + Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. + + A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. + DS: Probably better modeled as a role. + OBI + bead + assay bead + + + + + + + + + + + + + + + epitope + + a material entity bearing the epitope role + IEDB + IEDB + epitope + + + + + + + + + + An occurrence of disease is a process involving pathologic changes within an organism + IEDB + IEDB + + obsolete_occurrence of disease + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + host exposure to infectious agent + + a process in which an infectious agent comes into physical contact with a host organism. + IEDB + IEDB + host exposure to infectious agent + + + + + + + + + + + + + + + + + + + + + + + + + administration in vivo with infectious agent + + is an administration of an infectious agent to a host organism + IEDB + IEDB + administration in vivo with infectious agent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + occurrence of infectious disease + + Is an occurrence of a disease caused by an infection + IEDB + IEDB + occurrence of infectious disease + + + + + + + + + + + + + + + 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 + IEDB + disposition to cause an 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 + IEDB + allergic reaction + + + + + + + + + + + + + + + + + + + + + occurrence of allergy + + The process of an allergic disease occurring in an organism. + IEDB + IEDB + occurrence of allergy + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-2 production by T cells that uses an ELISPOT assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-2 production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + epitope binding by adaptive immune receptor + + + + + + + + + + + + + + + Immunization in vivo + + Process of administering an object playing the role of immunogen to a living organism + IEDB + IEDB + Immunization in vivo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + adaptive immune effector function + + + + + + + + + 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 + IEDB + IEDB + living with infected household contact + + + + + + + + + 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 + IEDB + IEDB + living in endemic area + + + + + + + + + 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 + IEDB + IEDB + pathogen release in laboratory accident + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Immunization in vitro + + Process of administering an object playing the role of immunogen to a cell culture + IEDB + IEDB + Immunization in vitro + + + + + + + + + + + + + + + + + + + + + infection process + + the detrimental process in which an infectious agent colonizes or replicates in a host environment + IEDB + IEDB + infection process + + + + + + + + + + + + + + + + + + adaptive immune receptor + + is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. + IEDB + IEDB + adaptive immune receptor + + + + + + + + + + + + + + + immunogen + + a material entity bearing the immunogen role + IEDB + IEDB + immunogen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + environmental exposure to infectious agent + + + + + + + + + + + + + + + + + + + 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. + IEDB + IEDB + host of immune response + + + + + + + + + 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. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl5008.html + 293-T 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)). + IEDB + IEDB + C1R cell line + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + experimental infection of cell culture + + + + + + + + + EL-4 cell line + + A cell line derived from mouse (C57BL/6N) lymphoma cells. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl1160.html + EL-4 cell line + + + + + + + + + HeLa cell culture + + A cell line derived from human cervical cancer cells. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl1597.html + HeLa cell line + + + + + + + + + JAWS II cell line + + 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 + JAWS II cell line + + + + + + + + + + + + + + + antigen + + is a material entity that has the antigen role + IEDB + IEDB + antigen + + + + + + + + + Jurkat cell line + + A cell line derived from human T cells. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl5296.html + Jurkat cell line + + + + + + + + + JY cell line + + The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) + IEDB + IEDB + JY cell line + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An immune epitope assay that detects T cell epitope recognition. + IEDB + IEDB + T cell binding|any method + assay measuring binding of a T cell epitope:MHC:TCR complex + + + + + + + + + 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. + IEDB + IEDB + RMA cell line + + + + + + + + + T2 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 + T2 cell line + + + + + + + + + infectious disease + + is a disease caused by an infectious agent + IEDB + IEDB + infectious disease + + + + + + + + + + + + + + + + + + + + + + + + + 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. + IEDB + IEDB + lymph node cell specimen + + + + + + + + + + + + + + + + + + + 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. + 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. + IEDB + adherent cell culture sample + IEDB + cultured adherent cell populaiton + + + + + + + + + + + + + + + + + + + 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). + IEDB + PBMC cell culture sample + IEDB + cultured PBMC cell population + + + + + + + + + + + + + + + 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 + IEDB + disposition to be bound by an adaptive immune receptor + + + + + + + + + organ harvesting + + The process of removing an organ from its source organism + IEDB + IEDB + organ harvesting + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured CD3+ T cell population + + A T cell population characterized by expressing the CD3 molecule on its surface. + IEDB + CD3+ T cell culture sample + IEDB + cultured CD3+ T cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured CD3- T cell population + + A T cell population characterized by not expressing the CD3 molecule on its surface. + IEDB + CD3- T cell culture sample + IEDB + cultured CD3- T cell population + + + + + + + + + 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 + IEDB + allergy + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured CD4- T cell population + + A T cell population characterized by not expressing the CD4 molecule on its surface. + IEDB + CD4- T cell culture sample + IEDB + cultured CD4- T cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured CD8- T cell population + + A T cell population characterized by not expressing the CD8 molecule on its surface. + IEDB + CD8- T cell culture sample + IEDB + cultured 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. + IEDB + CD4-/CD8- T cell culture sample + IEDB + cultured CD4-/CD8- T cell population + + + + + + + + + cancer + + A disease characterized by abnormal and uncontrolled cell division + IEDB + IEDB + cancer + + + + + + + + + autoimmune disease + + Is a disease characterized by an immune response of an organism against parts of itself + IEDB + IEDB + autoimmune disease + + + + + + + + + + placeholder to be imported from disease ontology + IEDB + IEDB + + + obsolete_disease + true + + + + + + + + + + + + + + + + + + + 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 + IEDB + epitope specific IL-2 release by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + MHC:epitope complex binding to TCR + + + + + + + + + + + + + + + + + + + An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ELISPOT + ELISPOT assay measuring epitope specific interferon-gamma production by T cells + + + + + + + + + exposure resulting in 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 + + + + + + + + + immunogen role + + any entity capable of eliciting an immune response when introduced to components of the immune system + IEDB + IEDB + immunogen 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. + IEDB + IEDB + host of immune response role + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + effector T cell 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. + antigen presentation function + + + + + + + + + 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 + IEDB + restricting MHC role + + + + + + + + + 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 + IEDB + Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. + donor + + + + + + + + + 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. + IEDB + IEDB + immune epitope carrier 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 + IEDB + adjuvant role + + + + + + + + + + + + + + + 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 + IEDB + disposition to infect an organism + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + IEDB + immunization + + + + + + + + + + + + + + + blood harvesting + + A material separation where blood is taken from an organism. + IEDB + IEDB + blood harvesting + + + + + + + + + L cell line + + A cell line derived from mouse fibroblasts. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl3075.html + L cell line + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + antigen presenting cell culture sample + IEDB + cultured antigen presenting cell population + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cultured effector T cell population + A culture of cytotoxic CD8+ T cells. + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + IEDB + environmental proximity to infectious agent + + + + + + + + + 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 + IEDB + IEDB + contact to pathogen carrying biological vector + + + + + + + + + + + + + + + + + + + + + + + + + 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. + IEDB + IEDB + splenocyte specimen + + + + + + + + + P815 cell line + + A cell line derived from mouse mastocytoma. + IEDB + IEDB + http://www.biotech.ist.unige.it/cldb/cl5244.html + P815 cell line + + + + + + + + + + + + + + + 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 + IEDB + assay antigen role + + + + + + + + + pathologic process + + abnormal, harmful processes caused by or associated with a disease + IEDB + IEDB + pathologic process + + + + + + + + + + + + + + + + + + + + + + + + A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + qualitative binding|binding assay + assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A MHC ligand assay that detects the binding of a ligand to an MHC molecule. + IEDB + IEDB + MHC binding|binding assay + assay measuring binding of a MHC:ligand complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An immune epitope assay that detects B cell epitope recognition. + IEDB + IEDB + antibody binding|any method + assay measuring binding of a B cell epitope:antibody complex + + + + + + + + + An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event + IEDB + IEDB + immune epitope assay + immune epitope assay + + + + + + + + + + + + + + + + + + + + A T cell epitope dependent biological activity assay that detects cytokine production. + IEDB + IEDB + cytokine release|biological activity + biological activity assay measuring epitope specific cytokine production by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 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 + + + + + + + + + + + + + + + + + + + An assay of epitope specific interferon-gamma production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ELISA + ELISA measuring epitope specific interferon-gamma production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-2 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-2 release|ELISA + ELISA measuring epitope specific interleukin-2 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-4 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ELISA + ELISA measuring epitope specific interleukin-4 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-5 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-5 release|ELISA + ELISA measuring epitope specific interleukin-5 production by T cells + + + + + + + + + + + + + + + + + + + A T cell epitope specific tumor necrosis factor production assay that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + TNFa release|ELISA + ELISA measuring epitope specific tumor necrosis factor production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-10 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ELISA + ELISA measuring epitope specific interleukin-10 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA. + 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 + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-6 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-6 release|ELISA + ELISA measuring epitope specific interleukin-6 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-13 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ELISA + ELISA measuring epitope specific interleukin-13 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-12 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-12 release|ELISA + ELISA measuring epitope specific interleukin-12 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-1b release|ELISA + ELISA measuring epitope specific interleukin-1 beta production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-17 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-17 release|ELISA + ELISA measuring epitope specific interleukin-17 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-18 production by T cells that uses an ELISA. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-18 release|ELISA + ELISA measuring epitope specific interleukin-18 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-4 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-4 production by T cells + + + + + + + + + + + + + + + + + + + A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay. + IEDB + IEDB + TNFa release|ELISPOT + ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-10 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-10 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IL-13 release|ELISPOT + ELISPOT assay measuring epitope specific interleukin-13 production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay. + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB + IFNg release|ICS + intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay. + 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 + + + + + + + + + + + + + + + + + + + A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay. + 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 + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay. + 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 + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay. + 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 + + + + + + + + + + + + + + + + + + + An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay. + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A T cell epitope qualitative binding assay that uses an MHC multimer staining assay. + 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 + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + epitope specific T cell proliferation + + A biological process where T cells proliferate resulting from the recognition of a T cell epitope. + IEDB + IEDB + epitope specific T cell proliferation + + + + + + + + + + + + + + + + + + + + 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 + IEDB + epitope specific GM-CSF 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 + IEDB + epitope specific IFN-g 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 + IEDB + epitope specific IL-10 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 + IEDB + epitope specific IL-12 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 + IEDB + epitope specific IL-13 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 + IEDB + epitope specific IL-17 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 + IEDB + epitope specific IL-18 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 + IEDB + epitope specific IL-1b 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 + IEDB + epitope specific IL-4 release by T cells + + + + + + + + + + + + + + + + + + + allergen + Birch pollen is an allergen + + A material entity bearing the disposition to cause an allergic reaction + IEDB + IEDB + allergen + + + + + + + + + + + + + + + + + + + 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 + IEDB + epitope specific IL-5 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 + IEDB + epitope specific IL-6 release 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 + IEDB + epitope specific killing 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 + IEDB + epitope specific TNF release by T cells + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + FFPE specimen + 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 + + + FFPE specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some uterine cervix + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + uterine cervix specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some urethra + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + urethra specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some cervical mucus + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + cervical mucus specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some throat + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + throat specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some eye + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + eye specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some respiratory system + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + respiratory system specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some upper respiratory tract + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + upper respiratory tract specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some nasopharynx + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + nasopharynx specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some semen + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + semen specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some bodily fluid + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + bodily fluid specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some chorionic villus + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + chorionic villus specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some meconium + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + meconium specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some umbilical cord blood + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + umbilical cord blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some arterial blood + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + arterial blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some venous blood + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + venous blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some capillary blood + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + capillary blood specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some erythrocytes + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + erythrocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some reticulocytes + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + reticulocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specimen that is derived from some leukocytes + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X + leukocyte specimen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + - - + + - + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - 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 - IEDB - environmental exposure to infectious agent + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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. - IEDB - IEDB - host of immune response - - - - - - - - - 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. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl5008.html - 293-T 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)). - IEDB - IEDB - C1R cell line - - - - - - - - + - + - - - - - - - - - + + + + - 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 - IEDB - experimental infection of cell culture - - - - - - - - - EL-4 cell line - - A cell line derived from mouse (C57BL/6N) lymphoma cells. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl1160.html - EL-4 cell line - - - - - - - - - HeLa cell culture - - A cell line derived from human cervical cancer cells. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl1597.html - HeLa cell line - - - - - - - - - JAWS II cell line - - 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 - JAWS II cell line - - - - - - - - - - - - - - - antigen - - is a material entity that has the antigen role - IEDB - IEDB - antigen - - - - - - - - - Jurkat cell line - - A cell line derived from human T cells. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl5296.html - Jurkat cell line - - - - - - - - - JY cell line - - The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) - IEDB - IEDB - JY cell line + 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 - + - - + + + - - + - + - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -76146,924 +103339,683 @@ Possible ecological risks of transgenic organism release when transgenes affect - - An immune epitope assay that detects T cell epitope recognition. - IEDB - IEDB - T cell binding|any method - assay measuring binding of a T cell epitope:MHC:TCR complex - - - - - - - - - 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. - IEDB - IEDB - RMA cell line - - - - - - - - - T2 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 - T2 cell line - - - - - - - - - infectious disease - - is a disease caused by an infectious agent - IEDB - IEDB - infectious disease - - - - - - - - + - + - - - - - - - - - + + + + - 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. - IEDB - IEDB - lymph node cell specimen + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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. - 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. - IEDB - adherent cell culture sample - IEDB - cultured adherent cell populaiton - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - 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). - IEDB - PBMC cell culture sample - IEDB - cultured PBMC cell population + + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - 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 - IEDB - disposition to be bound by an adaptive immune receptor - - - - - - - - - organ harvesting - - The process of removing an organ from its source organism - IEDB - IEDB - organ harvesting + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + - + - - + + + + + + - - cultured CD3+ T cell population - - A T cell population characterized by expressing the CD3 molecule on its surface. - IEDB - CD3+ T cell culture sample - IEDB - cultured CD3+ T cell population + + 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 - + - - + + + - - + - - - - - - - - - + + + + + - - - - cultured CD3- T cell population - - A T cell population characterized by not expressing the CD3 molecule on its surface. - IEDB - CD3- T cell culture sample - IEDB - cultured CD3- T cell population - - - - - - - - - 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 - IEDB - allergy - - - - - - - - - - - - + - - - - - - - - - + + + + + - - cultured CD4- T cell population - - A T cell population characterized by not expressing the CD4 molecule on its surface. - IEDB - CD4- T cell culture sample - IEDB - cultured CD4- T cell population - - - - - - - - + + - - + - - - - - - - - - + + + + + + + + + - - cultured CD8- T cell population - - A T cell population characterized by not expressing the CD8 molecule on its surface. - IEDB - CD8- T cell culture sample - IEDB - cultured CD8- T cell population + + 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 - + - - + + + - - + - - - - - - - - - - - - - - - - - + + + + + - - - - cultured CD4-/CD8- T cell population - - 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 - cultured CD4-/CD8- T cell population - - - - - - - - - cancer - - A disease characterized by abnormal and uncontrolled cell division - IEDB - IEDB - cancer - - - - - - - - - autoimmune disease - - Is a disease characterized by an immune response of an organism against parts of itself - IEDB - IEDB - autoimmune disease - - - - - - - - - - placeholder to be imported from disease ontology - IEDB - IEDB - - - obsolete_disease - true - - - - - - - - - - - - - + + + + + + + + + + + + - - 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 - IEDB - epitope specific IL-2 release by T cells - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - IEDB - MHC:epitope complex binding to TCR - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - An assay of epitope specific interferon-gamma production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ELISPOT - ELISPOT assay measuring epitope specific interferon-gamma production by T cells - - - - - - - - - exposure resulting in 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 - - - - - - - - - immunogen role - - any entity capable of eliciting an immune response when introduced to components of the immune system - IEDB - IEDB - immunogen 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. - IEDB - IEDB - host of immune response role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - IEDB - effector T cell 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. - antigen presentation function - - - - - - - - - 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 - IEDB - restricting MHC role - - - - - - - - - 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 - IEDB - Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended. - donor - - - - - - - - - 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. - IEDB - IEDB - immune epitope carrier role + + + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + - 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 - IEDB - adjuvant role + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + - 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 - IEDB - disposition to infect an organism + 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 - + - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + - + - - - - - - + - - + + + + + + - - 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 - IEDB - immunization + + 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 - + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - blood harvesting - - A material separation where blood is taken from an organism. - IEDB - IEDB - blood harvesting - - - - - - - - - L cell line - - A cell line derived from mouse fibroblasts. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl3075.html - L cell line - - - - - - - - + - - + - + - - + + + + + + - - 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 - antigen presenting cell culture sample - IEDB - cultured antigen presenting cell population + + 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 - + - - + + + - - + - + - - + + + + + + + + + + + + + + + + @@ -77071,289 +104023,199 @@ 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. - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - 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 - - - - - - - - - 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 - IEDB - environmental proximity to infectious agent - - - - - - - - - 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 - IEDB - IEDB - contact to pathogen carrying biological vector - - - - - - - - + - + - - - - - - - - - + + + + - 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. - IEDB - IEDB - splenocyte specimen - - - - - - - - - P815 cell line - - A cell line derived from mouse mastocytoma. - IEDB - IEDB - http://www.biotech.ist.unige.it/cldb/cl5244.html - P815 cell line + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - 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 - IEDB - assay antigen role - - - - - - - - - pathologic process - - abnormal, harmful processes caused by or associated with a disease - IEDB - IEDB - pathologic process - - - - - - - - - - + - + - - + + + + + + - - A T cell epitope recognition assay that qualitatively detects MHC:epitope complex binding to TCR. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - qualitative binding|binding assay - assay measuring qualitiative binding of a T cell epitope:MHC:TCR complex + + 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 - + - - + + + - + + + + + + + + + + + + + + - + - - + + + + + + + + - + - + - - - - - - - - - - - - + + + + + + - - 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 + + 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 - + - - + + + - - + - + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -77361,42 +104223,57 @@ 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|binding assay - assay measuring binding of a MHC:ligand complex + + + + + + + + + + + + + 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 - + - - + + + - - + - + - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -77404,78 +104281,57 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - - An immune epitope assay that detects B cell epitope recognition. - IEDB - IEDB - antibody binding|any method - assay measuring binding of a B cell epitope:antibody complex - - - - - - - - - An assay that detects the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event - IEDB - IEDB - immune epitope assay - immune epitope assay - - - - - - - - + - - - - - - - - - + + + + - A T cell epitope dependent biological activity assay that detects cytokine production. - IEDB - IEDB - cytokine release|biological activity - biological activity assay measuring epitope specific cytokine production by T cells + 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 - + - - + + + - - - + + + + + + + + + + + + - + - + - - + + @@ -77483,36 +104339,70 @@ 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 + + + + + + + + + + + + + + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + - + - + - - + + @@ -77520,1634 +104410,2547 @@ 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 - - - - - - - - - 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 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interferon-gamma production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ELISA - ELISA measuring epitope specific interferon-gamma production by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-2 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-2 release|ELISA - ELISA measuring epitope specific interleukin-2 production by T cells - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-4 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ELISA - ELISA measuring epitope specific interleukin-4 production by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-5 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-5 release|ELISA - ELISA measuring epitope specific interleukin-5 production by T cells + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - A T cell epitope specific tumor necrosis factor production assay that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - TNFa release|ELISA - ELISA measuring epitope specific tumor necrosis factor production by T cells + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-10 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ELISA - ELISA measuring epitope specific interleukin-10 production by T cells + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells that uses an ELISA. - 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 + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-6 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-6 release|ELISA - ELISA measuring epitope specific interleukin-6 production by T cells - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-13 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISA - ELISA measuring epitope specific interleukin-13 production by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-12 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-12 release|ELISA - ELISA measuring epitope specific interleukin-12 production by T cells - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-1 beta production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-1b release|ELISA - ELISA measuring epitope specific interleukin-1 beta production by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-17 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-17 release|ELISA - ELISA measuring epitope specific interleukin-17 production by T cells - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-18 production by T cells that uses an ELISA. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-18 release|ELISA - ELISA measuring epitope specific interleukin-18 production by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-4 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-4 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-4 production by T cells + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - A T cell epitope specific tumor necrosis factor production assay that uses an ELISPOT assay. - IEDB - IEDB - TNFa release|ELISPOT - ELISPOT assay measuring epitope specific tumor necrosis factor production by T cells - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-10 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-10 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-10 production by T cells + + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-13 production by T cells that uses an ELISPOT assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IL-13 release|ELISPOT - ELISPOT assay measuring epitope specific interleukin-13 production by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interferon-gamma production by T cells that uses an intracellular cytokine staining assay. - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB - IFNg release|ICS - intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-2 production by T cells that uses an intracellular cytokine staining assay. - 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 + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - A T cell epitope specific tumor necrosis factor production assay that uses an intracellular cytokine staining assay. - 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 + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-4 production by T cells that uses an intracellular cytokine staining assay. - 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 - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-10 production by T cells that uses an intracellular cytokine staining assay. - 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 + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - An assay of epitope specific interleukin-17 production by T cells that uses an intracellular cytokine staining assay. - 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 - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - A T cell epitope qualitative binding assay that uses an MHC multimer staining assay. - 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 + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - epitope specific T cell proliferation - - A biological process where T cells proliferate resulting from the recognition of a T cell epitope. - IEDB - IEDB - epitope specific T cell proliferation + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - 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 - IEDB - epitope specific GM-CSF 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 - IEDB - epitope specific IFN-g release by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - IEDB - epitope specific IL-10 release by T cells + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - IEDB - epitope specific IL-12 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 - IEDB - epitope specific IL-13 release by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - IEDB - epitope specific IL-17 release by T cells + + + + + + + + + + + + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - IEDB - epitope specific IL-18 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 - IEDB - epitope specific IL-1b release by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - IEDB - epitope specific IL-4 release by T cells - - - - - - - - + + - - - + + + + + + + + + + + + + + + + - - allergen - Birch pollen is an allergen - - A material entity bearing the disposition to cause an allergic reaction - IEDB - IEDB - allergen + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - IEDB - epitope specific IL-5 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 - IEDB - epitope specific IL-6 release by T cells + + 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 - + - - + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - 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 - IEDB - epitope specific killing 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 - IEDB - epitope specific TNF release by T cells + + 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 - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + - + - - + + + + + + - - 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 - - - - - - - - - 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 - - - - - - - - - FFPE specimen - 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 - - - FFPE specimen - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from some uterine cervix - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - uterine cervix specimen - - - - - - - - - - - - - - - - - - - - - - - - - - - A specimen that is derived from some urethra - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - urethra specimen + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some cervical mucus - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - cervical mucus specimen + + + + + + + + + + + + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some throat - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - throat specimen + + + + + + + + + + + + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some eye - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - eye specimen + + + + + + + + + + + + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some respiratory system - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - respiratory system specimen + + + + + + + + + + + + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some upper respiratory tract - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - upper respiratory tract specimen + + + + + + + + + + + + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some nasopharynx - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - nasopharynx specimen + + + + + + + + + + + + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some semen - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - semen specimen + + + + + + + + + + + + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some bodily fluid - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - bodily fluid specimen - - - - - - - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some chorionic villus - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - chorionic villus specimen + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some meconium - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - meconium specimen - - - - - - - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some umbilical cord blood - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - umbilical cord blood specimen + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some arterial blood - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - arterial blood specimen - - - - - - - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some venous blood - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - venous blood specimen + + 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 - + - - + + + - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - A specimen that is derived from some capillary blood - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - capillary blood specimen - - - - - - - + - - + - + - - + + + + + + - A specimen that is derived from some erythrocytes - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - erythrocyte specimen + 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 - + - + + - - + - + - - + + + + + + + + + + + + + + + + @@ -79156,42 +106959,35 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - A specimen that is derived from some reticulocytes - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - reticulocyte specimen - - - - - - - - - + - + - - + + + + + + - A specimen that is derived from some leukocytes - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - Mark A. Miller|ORCID:0000-0001-9076-6066|Christian Stoeckert|ORCID:0000-0002-5714-991X - leukocyte specimen + 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 @@ -79361,6 +107157,12 @@ realizes some 'host of immune response role' + + + + + + @@ -79405,6 +107207,12 @@ realizes some 'host of immune response role' + + + + + + @@ -79417,18 +107225,78 @@ realizes some 'host of immune response role' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -79479,6 +107347,54 @@ realizes some 'host of immune response role' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -79822,6 +107738,12 @@ realizes some 'host of immune response role' + + + + + + @@ -79864,6 +107786,12 @@ realizes some 'host of immune response role' + + + + + + @@ -80020,6 +107948,12 @@ realizes some 'host of immune response role' + + + + + + @@ -80038,12 +107972,24 @@ realizes some 'host of immune response role' + + + + + + + + + + + + @@ -80122,6 +108068,12 @@ realizes some 'host of immune response role' + + + + + + @@ -80405,19 +108357,8 @@ 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 @@ -80429,13 +108370,7 @@ realizes some 'host of immune response role' - - - - - - - + Thermo Philippe Rocca-Serra Thermo @@ -80446,13 +108381,7 @@ realizes some 'host of immune response role' - - - - - - - + Waters Philippe Rocca-Serra Waters @@ -80463,13 +108392,7 @@ realizes some 'host of immune response role' - - - - - - - + BIO-RAD Philippe Rocca-Serra BIO-RAD @@ -80491,13 +108414,7 @@ realizes some 'host of immune response role' - - - - - - - + Ambion Philippe Rocca-Serra Ambion @@ -80508,13 +108425,7 @@ realizes some 'host of immune response role' - - - - - - - + Helicos Philippe Rocca-Serra Helicos @@ -80525,13 +108436,7 @@ realizes some 'host of immune response role' - - - - - - - + Roche Philippe Rocca-Serra Roche @@ -80542,13 +108447,7 @@ realizes some 'host of immune response role' - - - - - - - + Illumina Philippe Rocca-Serra Illumina @@ -80615,13 +108514,7 @@ realizes some 'host of immune response role' - - - - - - - + Agilent Philippe Rocca-Serra Agilent @@ -80670,13 +108563,7 @@ realizes some 'host of immune response role' - - - - - - - + Li-Cor Philippe Rocca-Serra Li-Cor @@ -80687,13 +108574,7 @@ realizes some 'host of immune response role' - - - - - - - + Bruker Corporation Philippe Rocca-Serra Bruker Corporation @@ -80766,13 +108647,7 @@ realizes some 'host of immune response role' - - - - - - - + Applied Biosystems Philippe Rocca-Serra Applied Biosystems @@ -80809,13 +108684,7 @@ realizes some 'host of immune response role' - - - - - - - + Bruker Daltonics Philippe Rocca-Serra Bruker Daltonics @@ -80876,13 +108745,7 @@ realizes some 'host of immune response role' - - - - - - - + Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 @@ -81050,13 +108913,7 @@ realizes some 'host of immune response role' - - - - - - - + U.S. Food and Drug Administration FDA U.S. Food and Drug Administration @@ -81130,13 +108987,7 @@ realizes some 'host of immune response role' - - - - - - - + eBioscience A supplier of flow cytometry analyzers Karin Breuer @@ -81149,13 +109000,7 @@ realizes some 'host of immune response role' - - - - - - - + Cytopeia A supplier of flow cytometry analyzers Karin Breuer @@ -81168,13 +109013,7 @@ realizes some 'host of immune response role' - - - - - - - + Exalpha Biological A supplier of flow cytometry analyzers Karin Breuer @@ -81187,13 +109026,7 @@ realizes some 'host of immune response role' - - - - - - - + Apogee Flow Systems A supplier of flow cytometry analyzers Karin Breuer @@ -81206,13 +109039,7 @@ realizes some 'host of immune response role' - - - - - - - + Exbio Antibodies A supplier of flow cytometry analyzers Karin Breuer @@ -81225,13 +109052,7 @@ realizes some 'host of immune response role' - - - - - - - + Becton Dickinson (BD Biosciences) A supplier of flow cytometry analyzers Karin Breuer @@ -81244,13 +109065,7 @@ realizes some 'host of immune response role' - - - - - - - + Dako Cytomation A supplier of flow cytometry analyzers Karin Breuer @@ -81263,13 +109078,7 @@ realizes some 'host of immune response role' - - - - - - - + Millipore A supplier of flow cytometry analyzers Karin Breuer @@ -81282,13 +109091,7 @@ realizes some 'host of immune response role' - - - - - - - + Antigenix A supplier of flow cytometry analyzers Karin Breuer @@ -81301,13 +109104,7 @@ realizes some 'host of immune response role' - - - - - - - + Partec A supplier of flow cytometry analyzers Karin Breuer @@ -81320,13 +109117,7 @@ realizes some 'host of immune response role' - - - - - - - + Beckman Coulter A supplier of flow cytometry analyzers Karin Breuer @@ -81339,13 +109130,7 @@ realizes some 'host of immune response role' - - - - - - - + Advanced Instruments Inc. (AI Companies) A supplier of flow cytometry analyzers Karin Breuer @@ -81358,13 +109143,7 @@ realizes some 'host of immune response role' - - - - - - - + Miltenyi Biotec A supplier of flow cytometry analyzers Karin Breuer @@ -81377,13 +109156,7 @@ realizes some 'host of immune response role' - - - - - - - + AES Chemunex A supplier of flow cytometry analyzers Karin Breuer @@ -81396,13 +109169,7 @@ realizes some 'host of immune response role' - - - - - - - + Bentley Instruments A supplier of flow cytometry analyzers Karin Breuer @@ -81415,13 +109182,7 @@ realizes some 'host of immune response role' - - - - - - - + Invitrogen A supplier of flow cytometry analyzers Karin Breuer @@ -81434,13 +109195,7 @@ realizes some 'host of immune response role' - - - - - - - + Luminex A supplier of flow cytometry analyzers Karin Breuer @@ -81453,13 +109208,7 @@ realizes some 'host of immune response role' - - - - - - - + CytoBuoy A supplier of flow cytometry analyzers Karin Breuer @@ -81472,13 +109221,7 @@ realizes some 'host of immune response role' - - - - - - - + Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng @@ -81490,13 +109233,7 @@ 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 @@ -81508,13 +109245,7 @@ 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 @@ -83411,13 +111142,7 @@ 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 @@ -83427,6 +111152,19 @@ 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 + + + + diff --git a/views/obi.obo b/views/obi.obo index ca8eccff..0e796654 100644 --- a/views/obi.obo +++ b/views/obi.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: obi/2020-12-16/obi.obo -date: 16:12:2020 12:33 +data-version: obi/2021-04-06/obi.obo +date: 06:04:2021 10:16 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 property_value: defaultLanguage "en" 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 "2020-12-16" xsd:string +property_value: owl:versionInfo "2021-04-06" xsd:string [Term] id: APOLLO_SV:00000008 @@ -332,12 +332,54 @@ name: biotin def: "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." [] is_a: OBI:0002744 ! molecular label +[Term] +id: CHEBI:16113 +name: cholesterol +def: "A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:16134 +name: ammonia +def: "An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:16526 +name: carbon dioxide +def: "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." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:16670 name: peptide def: "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." [] is_a: CHEBI:33839 ! macromolecule +[Term] +id: CHEBI:166899 +name: globulin type +def: "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." [] +is_a: CHEBI:33839 ! macromolecule + +[Term] +id: CHEBI:16737 +name: creatinine +def: "A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:168396 +name: mycophenolic acid +def: "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." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:16990 +name: bilirubin IXalpha +def: "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." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:16991 name: deoxyribonucleic acid @@ -349,18 +391,60 @@ id: CHEBI:17137 name: hydrogensulfite is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:17230 +name: homocysteine +def: "A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain." [] +is_a: CHEBI:33709 ! amino acid + [Term] id: CHEBI:17234 name: glucose def: "An aldohexose used as a source of energy and metabolic intermediate." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:17423 +name: methemoglobin +def: "A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin." [] +is_a: CHEBI:33839 ! macromolecule + +[Term] +id: CHEBI:17544 +name: hydrogencarbonate +def: "The carbon oxoanion resulting from the removal of a proton from carbonic acid." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:17650 +name: cortisol +def: "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" [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:17709 name: 5'-adenylyl sulfate def: "An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:17855 +name: triglyceride +def: "Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:17996 +name: chloride +def: "A halide anion formed when chlorine picks up an electron to form an an anion." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:20067 +name: 3-hydroxybutyric acid +def: "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." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:23367 name: molecular entity @@ -384,29 +468,87 @@ name: proton def: "Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:24875 +name: iron cation +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:25078 name: luciferin def: "A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:2637 +name: amikacin +def: "An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:26710 name: sodium chloride def: "An inorganic chloride salt having sodium(1+) as the counterion." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:27226 +name: uric acid +def: "An oxopurine that is the final oxidation product of purine metabolism." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:27889 name: lead(0) is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:28001 +name: vancomycin +def: "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." [] +is_a: CHEBI:16670 ! peptide + +[Term] +id: CHEBI:28358 +name: rac-lactic acid +def: "A racemate comprising equimolar amounts of (R)- and (S)-lactic acid." [] +is_a: BFO:0000040 ! material entity + [Term] id: CHEBI:28619 name: acrylamide def: "A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:28689 +name: dehydroepiandrosterone +def: "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." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:28774 +name: 3,3',5'-triiodothyronine +is_a: CHEBI:33709 ! amino acid + +[Term] +id: CHEBI:28864 +name: tobramycin +def: "A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:29101 +name: sodium(1+) +def: "A monoatomic monocation obtained from sodium." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:29103 +name: potassium(1+) +def: "A monoatomic monocation obtained from potassium." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:29191 name: hydroxyl @@ -419,6 +561,12 @@ def: "The stable isotope of hydrogen with relative atomic mass 2.014102 and a na is_a: CHEBI:23367 ! molecular entity is_a: CHEBI:33250 ! atom +[Term] +id: CHEBI:30660 +name: thyroxine +def: "An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions." [] +is_a: CHEBI:33709 ! amino acid + [Term] id: CHEBI:30682 name: ruthenium atom @@ -460,6 +608,11 @@ name: atom def: "A chemical entity constituting the smallest component of an element having the chemical properties of the element." [] is_a: BFO:0000040 ! material entity +[Term] +id: CHEBI:33262 +name: elemental oxygen +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:33321 name: rare earth metal atom @@ -506,17 +659,34 @@ def: "A macromolecule is a molecule of high relative molecular mass, the structu synonym: "polymer" EXACT [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:35143 +name: hemoglobin +is_a: CHEBI:33839 ! macromolecule + [Term] id: CHEBI:35729 name: gadolinium molecular entity is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:35780 +name: phosphate ion +def: "A phosphorus oxoanion that is the conjugate base of phosphoric acid." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:37333 name: gadodiamide def: "A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI)." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:37445 +name: folic acids +def: "A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:37586 name: sodium phosphate @@ -546,6 +716,23 @@ id: CHEBI:37989 name: Cy5 dye is_a: OBI:0002744 ! molecular label +[Term] +id: CHEBI:39123 +name: calcium cation +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:39127 +name: magnesium cation +def: "Any magnesium ion that is positively charged." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:39867 +name: valproic acid +def: "A branched-chain saturated fatty acid that comprises of a propyl substituent on a pentanoic acid stem." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:42098 name: digoxigenin @@ -557,6 +744,12 @@ id: CHEBI:42191 name: ethylenediaminetetraacetic acid is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:4551 +name: digoxin +def: "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." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:4705 name: double-stranded DNA @@ -568,6 +761,18 @@ name: 5-bromo-2'-deoxyuridine def: "A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:47774 +name: low-density lipoprotein cholesterol +def: "Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL)." [] +is_a: CHEBI:23367 ! molecular entity + +[Term] +id: CHEBI:47775 +name: high-density lipoprotein cholesterol +def: "Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL)." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:50076 name: chromium-51 @@ -644,12 +849,29 @@ name: bromophenol blue def: "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." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:61057 +name: tacrolimus hydrate +def: "A hydrate that is the monohydrate form of tacrolimus." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:61073 name: oxygen radical def: "An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species." [] is_a: CHEBI:23367 ! molecular entity +[Term] +id: CHEBI:81567 +name: thyroid stimulating hormone +is_a: CHEBI:33839 ! macromolecule + +[Term] +id: CHEBI:86319 +name: 25-hydroxyvitamin D2 +def: "A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group." [] +is_a: CHEBI:23367 ! molecular entity + [Term] id: CHEBI:9754 name: tris @@ -740,6 +962,13 @@ name: epithelial cell def: "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." [] is_a: CL:0000000 ! cell +[Term] +id: CL:0000077 +name: mesothelial cell +def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [] +is_a: CL:0000003 ! native cell +is_a: CL:0000066 ! epithelial cell + [Term] id: CL:0000084 name: T cell @@ -764,6 +993,12 @@ name: erythrocyte def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen." [] is_a: CL:0000000 ! cell +[Term] +id: CL:0000233 +name: platelet +def: "A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." [] +is_a: CL:0000003 ! native cell + [Term] id: CL:0000235 name: macrophage @@ -773,7 +1008,6 @@ 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] @@ -794,12 +1028,39 @@ name: lymphocyte def: "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." [] is_a: CL:0000842 ! mononuclear cell +[Term] +id: CL:0000556 +name: megakaryocyte +def: "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." [] +is_a: CL:0000003 ! native cell + [Term] id: CL:0000558 name: reticulocyte def: "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." [] is_a: CL:0000000 ! cell +[Term] +id: CL:0000560 +name: band form neutrophil +def: "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." [] +is_a: CL:0000775 ! neutrophil + +[Term] +id: CL:0000562 +name: nucleate erythrocyte +def: "An erythrocyte having a nucleus." [] +is_a: CL:0000003 ! native cell +is_a: CL:0000232 ! erythrocyte + +[Term] +id: CL:0000576 +name: monocyte +def: "Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells." [] +is_a: CL:0000003 ! native cell +is_a: CL:0000738 ! leukocyte +is_a: CL:0000842 ! mononuclear cell + [Term] id: CL:0000578 name: experimentally modified cell in vitro @@ -831,6 +1092,20 @@ name: basophil def: "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." [] is_a: CL:0000000 ! cell +[Term] +id: CL:0000771 +name: eosinophil +def: "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." [] +is_a: CL:0000003 ! native cell +is_a: CL:0000738 ! leukocyte + +[Term] +id: CL:0000775 +name: neutrophil +def: "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." [] +is_a: CL:0000003 ! native cell +is_a: CL:0000738 ! leukocyte + [Term] id: CL:0000786 name: plasma cell @@ -855,12 +1130,36 @@ name: mature NK T cell def: "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." [] is_a: CL:0000789 ! alpha-beta T cell +[Term] +id: CL:0000836 +name: promyelocyte +def: "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." [] +is_a: CL:0000003 ! native cell + [Term] id: CL:0000842 name: mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [] is_a: CL:0000000 ! cell +[Term] +id: CL:0002192 +name: metamyelocyte +def: "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." [] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0002193 +name: myelocyte +def: "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." [] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0011114 +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: CLO:0000001 name: cell line cell @@ -868,20 +1167,17 @@ is_a: OBI:0001866 ! secondary cultured cell [Term] id: CLO:0000018 -name: mortal cell line cell -def: "A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence." [] +name: 非永生细胞系细胞 is_a: CLO:0000001 ! cell line cell [Term] id: CLO:0000019 name: immortal cell line cell -def: "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." [] is_a: CLO:0000001 ! cell line cell [Term] id: CLO:0000031 name: cell line -def: "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). " [] is_a: OBI:0001905 ! secondary cultured cell population [Term] @@ -993,8 +1289,6 @@ is_a: GO:0001816 ! cytokine production [Term] id: GO:0002390 -name: platelet activating factor production -def: "The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] @@ -1027,6 +1321,12 @@ name: cytokine production involved in inflammatory response def: "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." [] is_a: GO:0001816 ! cytokine production +[Term] +id: GO:0003094 +name: glomerular filtration +def: "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." [] +is_a: GO:0008150 ! biological_process + [Term] id: GO:0003674 name: molecular_function @@ -1075,6 +1375,12 @@ name: cellular_component def: "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)." [] is_a: BFO:0000040 ! material entity +[Term] +id: GO:0005577 +name: fibrinogen complex +def: "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." [] +is_a: GO:0032991 ! protein-containing complex + [Term] id: GO:0005694 name: chromosome @@ -1247,7 +1553,7 @@ is_a: GO:0001816 ! cytokine production [Term] id: GO:0032602 name: chemokine production -def: "The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] +def: "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." [] is_a: GO:0001816 ! cytokine production [Term] @@ -1469,7 +1775,7 @@ is_a: GO:0001816 ! cytokine production [Term] id: GO:0032640 name: tumor necrosis factor production -def: "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." [] +def: "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." [] synonym: "TNF alpha production" EXACT [] is_a: GO:0071706 ! tumor necrosis factor superfamily cytokine production @@ -1660,8 +1966,8 @@ is_a: GO:0001816 ! cytokine production [Term] id: GO:0044808 -name: Oncostatin M production -def: "The appearance of Oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] +name: oncostatin M production +def: "The appearance of oncostatin M 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] @@ -1694,6 +2000,12 @@ name: carboxylic ester hydrolase activity def: "Catalysis of the hydrolysis of a carboxylic ester bond." [] is_a: GO:0003824 ! catalytic activity +[Term] +id: GO:0070288 +name: ferritin complex +def: "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." [] +is_a: GO:0032991 ! protein-containing complex + [Term] id: GO:0070358 name: actin polymerization-dependent cell motility @@ -1766,6 +2078,30 @@ name: tumor necrosis factor superfamily cytokine production def: "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." [] is_a: GO:0001816 ! cytokine production +[Term] +id: GO:0071735 +name: IgG immunoglobulin complex +def: "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." [] +is_a: GO:0019814 ! immunoglobulin complex + +[Term] +id: GO:0071742 +name: IgE immunoglobulin complex +def: "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." [] +is_a: GO:0019814 ! immunoglobulin complex + +[Term] +id: GO:0071745 +name: IgA immunoglobulin complex +def: "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." [] +is_a: GO:0019814 ! immunoglobulin complex + +[Term] +id: GO:0071753 +name: IgM immunoglobulin complex +def: "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." [] +is_a: GO:0019814 ! immunoglobulin complex + [Term] id: GO:0071924 name: chemokine (C-C motif) ligand 22 production @@ -4747,7 +5083,7 @@ is_a: BFO:0000023 ! role id: OBI:0000418 name: measuring glucose concentration in blood serum assay def: "An assay that determines the concentration of glucose molecules in a blood serum sample" [] -is_a: OBI:0000443 ! analyte assay +is_a: OBI:2100020 ! glucose assay [Term] id: OBI:0000419 @@ -5591,6 +5927,8 @@ is_a: OBI:0000832 ! measurement device id: OBI:0000566 name: NMR instrument def: "An Instrument which is used to carry out a NMR analysis of some sample." [] +synonym: "magnetic resonance imaging scanner" EXACT [] +synonym: "MRI scanner" EXACT [] synonym: "NMR instrument" EXACT [] is_a: OBI:0000832 ! measurement device @@ -9957,6 +10295,7 @@ id: OBI:0001318 name: proteomic profiling by array assay def: "An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology." [] is_a: OBI:0001985 ! microarray assay +is_a: OBI:2100023 ! protein assay [Term] id: OBI:0001319 @@ -18673,6 +19012,252 @@ def: "Procedure using suction, usually with a thin needle and syringe, to remove synonym: "aspiration procedure" EXACT [] is_a: OBI:0000659 ! specimen collection process +[Term] +id: OBI:0002786 +name: personal protective device +def: "A device which is a wearable garment designed to protect the wearer's body from injury or infection." [] +synonym: "personal protective equipment" EXACT [] +synonym: "PPE" EXACT [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0002787 +name: face mask +def: "A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles." [] +synonym: "face covering" EXACT [] +synonym: "respirator" EXACT [] +is_a: OBI:0002786 ! personal protective device + +[Term] +id: OBI:0002788 +name: non-medical mask +def: "A face mask not manufactured according to medical equipment standards." [] +synonym: "cloth mask" EXACT [] +is_a: OBI:0002787 ! face mask + +[Term] +id: OBI:0002789 +name: medical mask +def: "A face mask manufactured according to a recognized medical equipment standard." [] +synonym: "surgical mask" EXACT [] +is_a: OBI:0002787 ! face mask + +[Term] +id: OBI:0002790 +name: N95 respirator +def: "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." [] +synonym: "N95" EXACT [] +synonym: "N95 face mask" EXACT [] +synonym: "N95 facemask" EXACT [] +synonym: "N95 respirator mask" EXACT [] +is_a: OBI:0002787 ! face mask + +[Term] +id: OBI:0002791 +name: face shield +def: "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." [] +synonym: "faceshield" EXACT [] +synonym: "splash shield" EXACT [] +is_a: OBI:0002786 ! personal protective device + +[Term] +id: OBI:0002792 +name: patient gown +def: "A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff." [] +synonym: "hospital gown" EXACT [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002793 +name: scrubs +def: "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." [] +synonym: "scrub clothing item" EXACT [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002794 +name: reusable patient gown +def: "A patient gown intended to be reused after being laundered." [] +is_a: OBI:0002792 ! patient gown + +[Term] +id: OBI:0002795 +name: disposable patient gown +def: "A patient gown intended for a single period of continuous use and then disposed of." [] +is_a: OBI:0002792 ! patient gown + +[Term] +id: OBI:0002796 +name: medical gown +def: "A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional." [] +synonym: "hospital gown" EXACT [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002797 +name: apron +def: "A garment which is worn over other clothing and covers mainly the front of the body." [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0002798 +name: surgical gown +def: "A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures." [] +is_a: OBI:0002796 ! medical gown + +[Term] +id: OBI:0002799 +name: personal protective glove +def: "A personal protective device which is a glove." [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002800 +name: personal protective clothing item +def: "A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing." [] +is_a: OBI:0002786 ! personal protective device + +[Term] +id: OBI:0002802 +name: laboratory coat +def: "A personal protective clothing item which is an overcoat worn by medical or laboratory professionals." [] +synonym: "white coat" EXACT [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002803 +name: medical glove +def: "A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients." [] +is_a: OBI:0002799 ! personal protective glove + +[Term] +id: OBI:0002804 +name: nitrile glove +def: "A personal protective glove which is made out of nitrile rubber." [] +is_a: OBI:0002799 ! personal protective glove + +[Term] +id: OBI:0002805 +name: transparent droplet barrier +def: "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." [] +synonym: "transparent partition" EXACT [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0002806 +name: footwear cover +def: "A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants." [] +synonym: "boot cover" EXACT [] +synonym: "shoe cover" EXACT [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002807 +name: disposable footwear cover +def: "A footwear cover which is designed for a single period of continuous use and then disposed of." [] +is_a: OBI:0002806 ! footwear cover + +[Term] +id: OBI:0002808 +name: reusable footwear cover +def: "A footwear cover which is designed for repeated use." [] +is_a: OBI:0002806 ! footwear cover + +[Term] +id: OBI:0002809 +name: surgical N95 respirator +def: "A N95 respirator which has been approved by the FDA as a surgical mask." [] +synonym: "healthcare respirator" EXACT [] +synonym: "medical respirator" EXACT [] +synonym: "surgical N95" EXACT [] +synonym: "surgical N95 respirator" EXACT [] +is_a: OBI:0002790 ! N95 respirator + +[Term] +id: OBI:0002810 +name: protective coverall +def: "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." [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002811 +name: protective sleeve +def: "A personal protective clothing item which is a protective cover worn over the arm." [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002812 +name: protective apron +def: "A personal protective clothing item which is an apron." [] +is_a: OBI:0002797 ! apron +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002813 +name: medical cap +def: "A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp." [] +synonym: "bouffant cap" EXACT [] +synonym: "bouffant hat" EXACT [] +synonym: "medical bonnet" EXACT [] +synonym: "scrub cap" EXACT [] +synonym: "surgical hat" EXACT [] +is_a: OBI:0002800 ! personal protective clothing item + +[Term] +id: OBI:0002814 +name: specimen collection device +def: "A container used to collect a specimen." [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0002819 +name: specimen pad +def: "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." [] +synonym: "absorbant pad" EXACT [] +synonym: "polysponge" EXACT [] +synonym: "sample pad" EXACT [] +synonym: "sampling sponge" EXACT [] +synonym: "specimen sponge" EXACT [] +synonym: "surface wipe" EXACT [] +synonym: "swab" EXACT [] +is_a: OBI:0002814 ! specimen collection device + +[Term] +id: OBI:0002820 +name: specimen collection swab stick +def: "A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material." [] +synonym: " sponge stick" EXACT [] +synonym: "polyprobe" EXACT [] +synonym: "sponge probe" EXACT [] +synonym: "sponge-stick" EXACT [] +is_a: OBI:0002814 ! specimen collection device + +[Term] +id: OBI:0002821 +name: cotton swab +def: "A device which is a cotton pad mounted on one or both ends of a stick." [] +synonym: "Q-tip" EXACT [] +synonym: "swab-sampler" EXACT [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0002822 +name: drag swab +def: "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" [] +is_a: OBI:0002814 ! specimen collection device + +[Term] +id: OBI:0002823 +name: pre-moistened swab stick +def: "A specimen collection swab stick that is pre-moistened with liquid prior to sampling." [] +is_a: OBI:0002820 ! specimen collection swab stick + +[Term] +id: OBI:0002824 +name: surface wipe +def: "A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces." [] +is_a: OBI:0002814 ! specimen collection device + [Term] id: OBI:0002897 name: surveillance process @@ -19015,39 +19600,391 @@ def: "A specimen that derives from a biofilm that forms on the inner surface of is_a: OBI:0001479 ! specimen from organism [Term] -id: OBI:0005246 -name: injection function -def: "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." [] -is_a: BFO:0000034 ! function +id: OBI:0002975 +name: input protein sequence start site +def: "The position of the first amino acid in a protein sequence being analyzed (input protein sequence)." [] +synonym: "input protein start" EXACT [] +synonym: "query protein start site" EXACT [] +is_a: OBI:0000973 ! sequence data [Term] -id: OBI:0100010 -name: Epstein Barr virus transformed B cell -def: "A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity" [] -is_a: OBI:0000047 ! processed material +id: OBI:0002976 +name: input protein sequence stop site +def: "The position of the last amino acid in a protein sequence being analyzed (input protein sequence)." [] +synonym: "input protein stop" EXACT [] +synonym: "query protein stop site" EXACT [] +is_a: OBI:0000973 ! sequence data [Term] -id: OBI:0100014 -name: chimera -def: "An organism which contains cells or tissues with a different genotype" [] -is_a: OBI:0100026 ! organism +id: OBI:0002977 +name: input gene sequence start site +def: "The position of the first nucleotide in a gene sequence being analyzed (input gene sequence)." [] +synonym: "input gene start" EXACT [] +synonym: "query gene start site" EXACT [] +is_a: OBI:0000973 ! sequence data [Term] -id: OBI:0100015 -name: obsolete_anatomical entity -def: "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'" [] -is_a: ObsoleteClass ! Obsolete Class -is_obsolete: true +id: OBI:0002978 +name: input gene sequence stop site +def: "The position of the last nucelotide in a gene sequence being analyzed (input gene sequence)." [] +synonym: "input gene stop" EXACT [] +synonym: "query gene stop site" EXACT [] +is_a: OBI:0000973 ! sequence data [Term] -id: OBI:0100016 -name: blood plasma specimen -def: "a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended." [] -synonym: "plasma" EXACT [] -is_a: OBI:0000953 ! processed specimen +id: OBI:0002979 +name: reference protein sequence start site +def: "The position of the first amino acid in a reference protein sequence (sequence being used for comparison)." [] +synonym: "reference protein start" EXACT [] +synonym: "subject protein start site" EXACT [] +is_a: OBI:0000973 ! sequence data [Term] -id: OBI:0100017 +id: OBI:0002980 +name: reference protein sequence stop site +def: "The position of the last amino acid in a reference protein sequence (sequence being used for comparison)." [] +synonym: "reference protein stop" EXACT [] +synonym: "subject protein stop site" EXACT [] +is_a: OBI:0000973 ! sequence data + +[Term] +id: OBI:0002981 +name: reference gene sequence start site +def: "The position of the first nucleotide in a reference gene sequence (sequence being used for comparison)." [] +synonym: "reference gene start" EXACT [] +synonym: "subject gene start site" EXACT [] +is_a: OBI:0000973 ! sequence data + +[Term] +id: OBI:0002982 +name: reference gene sequence stop site +def: "The position of the last nucelotide in a reference sequence (sequence being used for comparison)." [] +synonym: "reference gene stop" EXACT [] +synonym: "subject gene stop site" EXACT [] +is_a: OBI:0000973 ! sequence data + +[Term] +id: OBI:0002983 +name: altitude measurement datum +def: "A length measurement datum between a point at sea or ground level and some point above it." [] +is_a: IAO:0000408 ! length measurement datum + +[Term] +id: OBI:0002984 +name: capture Hi-C assay +def: "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." [] +synonym: "cHi-C" EXACT [] +is_a: OBI:0002440 ! Hi-C assay + +[Term] +id: OBI:0002985 +name: magnetic resonance imaging assay +def: "An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity." [] +synonym: "MRI" EXACT [] +is_a: OBI:0000185 ! imaging assay + +[Term] +id: OBI:0002986 +name: computed tomography imaging assay +def: "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." [] +synonym: "CAT scan" EXACT [] +synonym: "computed tomography scan" EXACT [] +synonym: "CT scan" EXACT [] +is_a: OBI:0000185 ! imaging assay + +[Term] +id: OBI:0002987 +name: positron emission tomography imaging assay +def: "An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity." [] +synonym: "PET scan" EXACT [] +synonym: "positron emission tomography scan" EXACT [] +is_a: OBI:0000185 ! imaging assay + +[Term] +id: OBI:0002988 +name: specimen collection duration +def: "A time measurement datum that is the count of collection cycles over which a specimen collection process occurs." [] +synonym: "specimen collection duration" EXACT [] +is_a: IAO:0000416 ! time measurement datum + +[Term] +id: OBI:0002989 +name: material supplier +def: "A person or organization that provides material supplies to other people or organizations." [] +is_a: BFO:0000040 ! material entity + +[Term] +id: OBI:0002990 +name: T cell receptor repertoire sequencing assay +def: "A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample." [] +synonym: "TCR repertoire sequencing assay" EXACT [] +is_a: OBI:0600047 ! sequencing assay + +[Term] +id: OBI:0002991 +name: B cell receptor repertoire sequencing assay +def: "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." [] +synonym: "Antibody repertoire sequencing assay" EXACT [] +synonym: "BCR repertoire sequencing assay" EXACT [] +is_a: OBI:0600047 ! sequencing assay + +[Term] +id: OBI:0002992 +name: prevalence of pathogen in specimens +def: "A data item that is the frequency of detection of a specified pathogenic organism in collected specimens." [] +synonym: "prevalence of pathogen" EXACT [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0002993 +name: prevalence of blood meal specimens from a host organism +def: "A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens." [] +synonym: "host blood index" EXACT [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0002994 +name: presence of blood from host organism in blood meal specimen +def: "A data item that indicates whether blood in a blood meal specimen came from a specified host organism." [] +synonym: "presence of blood meal host organism" EXACT [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0002995 +name: blood meal source organism +def: "An organism that is the source of a blood meal." [] +synonym: "blood meal host organism" EXACT [] +is_a: OBI:0100026 ! organism + +[Term] +id: OBI:0002996 +name: blood meal source role +def: "A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism." [] +is_a: BFO:0000023 ! role + +[Term] +id: OBI:0002997 +name: arthropod attractor role +def: "A role of a material entity realized in drawing an arthropod in the direction of the material." [] +synonym: "attractant" EXACT [] +is_a: BFO:0000023 ! role + +[Term] +id: OBI:0002998 +name: arthropod collection process with automated identification +def: "An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected." [] +is_a: OBI:0002913 ! arthropod specimen collection process + +[Term] +id: OBI:0002999 +name: gravid female arthropod specimen collection process +def: "An arthropod specimen collection process that has the objective of collecting gravid female arthropods." [] +is_a: OBI:0002913 ! arthropod specimen collection process + +[Term] +id: OBI:0003000 +name: resting flight-capable arthropod specimen collection process +def: "An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity." [] +is_a: OBI:0002913 ! arthropod specimen collection process + +[Term] +id: OBI:0003001 +name: daytime arthropod specimen collection by aspiration +def: "An arthropod specimen collection by aspiration that occurs in the daytime." [] +is_a: OBI:0002912 ! arthropod specimen collection by aspiration + +[Term] +id: OBI:0003002 +name: arthropod resting in human house specimen collection by aspiration +def: "An arthropod specimen collection by aspiration that catches specimens resting inside a human house." [] +is_a: OBI:0002912 ! arthropod specimen collection by aspiration + +[Term] +id: OBI:0003003 +name: landing arthropod specimen collection process +def: "An arthropod specimen collection process that occurs while the arthropods land on a surface." [] +synonym: "collection of landing insects" EXACT [] +is_a: OBI:0002904 ! adult arthropod specimen collection process + +[Term] +id: OBI:0003004 +name: flying adult arthropod collection process by passive interception +def: "An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap." [] +is_a: OBI:0002904 ! adult arthropod specimen collection process + +[Term] +id: OBI:0003005 +name: device for resting of adult arthropods for collection +def: "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." [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0003006 +name: well net for arthropod immatures +def: "A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net." [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0003007 +name: arthropod trap containing small non-human animal bait +def: "An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller." [] +synonym: "trap containing small non-human animal bait" EXACT [] +is_a: OBI:0002920 ! arthropod trap + +[Term] +id: OBI:0003008 +name: trap for emerging adult arthropods +def: "An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage." [] +is_a: OBI:0002920 ! arthropod trap + +[Term] +id: OBI:0003009 +name: ferritin assay +def: "An assay that measures ferritin" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003010 +name: fibrinogen assay +def: "An assay that measures fibrinogen" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003011 +name: iron assay +def: "An analyte assay that measures the abundance of iron" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003012 +name: ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003013 +name: transferrin assay +def: "An analyte assay that measures the abundance of transferrin" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:0003014 +name: uric acid assay +def: "An analyte assay that measures the abundance of uric acid" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003015 +name: globulin assay +def: "An analyte assay that measures the abundance of globulin" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:0003016 +name: myelocyte assay +def: "A cytometry assay that measures the abundance and/or characteristics of myelocytes" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003017 +name: metamyelocyte assay +def: "A cytometry assay that measures the abundance and/or characteristics of metamyelocytes" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003018 +name: hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003019 +name: promyelocyte assay +def: "A cytometry assay that measures the abundance and/or characteristics of promyelocytes" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003021 +name: basophil assay +def: "A cytometry assay that measures the abundance and/or characteristics of basophils" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003022 +name: neutrophil assay +def: "A cytometry assay that measures the abundance and/or characteristics of neutrophils" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003023 +name: eosinophil assay +def: "A cytometry assay that measures the abundance and/or characteristics of eosinophils" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003024 +name: lymphocyte assay +def: "A cytometry assay that measures the abundance and/or characteristics of lymphocytes" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003025 +name: monocyte assay +def: "A cytometry assay that measures the abundance and/or characteristics of monocytes" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003026 +name: reticulocyte assay +def: "A cytometry assay that measures the abundance and/or characteristics of reticulocytes" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003027 +name: macrophage assay +def: "A cytometry assay that measures the abundance and/or characteristics of macrophages" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0003028 +name: platelet assay +def: "A cytometry assay that measures the abundance and/or characteristics of platelets" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0005246 +name: injection function +def: "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." [] +is_a: BFO:0000034 ! function + +[Term] +id: OBI:0100010 +name: Epstein Barr virus transformed B cell +def: "A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity" [] +is_a: OBI:0000047 ! processed material + +[Term] +id: OBI:0100014 +name: chimera +def: "An organism which contains cells or tissues with a different genotype" [] +is_a: OBI:0100026 ! organism + +[Term] +id: OBI:0100015 +name: obsolete_anatomical entity +def: "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'" [] +is_a: ObsoleteClass ! Obsolete Class +is_obsolete: true + +[Term] +id: OBI:0100016 +name: blood plasma specimen +def: "a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended." [] +synonym: "plasma" EXACT [] +is_a: OBI:0000953 ! processed specimen + +[Term] +id: OBI:0100017 name: blood serum specimen def: "A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors." [] is_a: OBI:0000953 ! processed specimen @@ -23071,115 +24008,2539 @@ def: "A specimen that is derived from some leukocytes" [] is_a: OBI:0002599 ! swab specimen [Term] -id: OBI:9999994 -name: chromium release assay -def: "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." [] -is_a: OBI:0000903 ! in vitro cell killing assay +id: OBI:2100001 +name: carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide" [] +is_a: OBI:0000443 ! analyte assay [Term] -id: OGMS:0000015 -name: clinical history -def: "A series of statements representing health-relevant qualities of a patient and of a patient's family." [] -is_a: IAO:0000030 ! information content entity +id: OBI:2100002 +name: sodium(1+) assay +def: "An analyte assay that measures the abundance of sodium(1+)" [] +is_a: OBI:0000443 ! analyte assay [Term] -id: OGMS:0000023 -name: phenotype -def: "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." [] -is_a: BFO:0000019 ! quality +id: OBI:2100003 +name: creatinine assay +def: "An analyte assay that measures the abundance of creatinine" [] +is_a: OBI:0000443 ! analyte assay [Term] -id: OGMS:0000031 -name: disease -def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] -is_a: BFO:0000016 ! disposition +id: OBI:2100004 +name: potassium(1+) assay +def: "An analyte assay that measures the abundance of potassium(1+)" [] +is_a: OBI:0000443 ! analyte assay [Term] -id: OGMS:0000063 -name: disease course -def: "The totality of all processes through which a given disease instance is realized." [] -is_a: GO:0008150 ! biological_process +id: OBI:2100005 +name: basophil count assay +def: "A cytometry assay that measures the count of basophils" [] +is_a: OBI:0003021 ! basophil assay [Term] -id: OGMS:0000073 -name: diagnosis -def: "The representation of a conclusion of a diagnostic process." [] -is_a: IAO:0000027 ! data item +id: OBI:2100006 +name: neutrophil count assay +def: "A cytometry assay that measures the count of neutrophils" [] +is_a: OBI:0003022 ! neutrophil assay [Term] -id: OGMS:0000090 -name: treatment -def: "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate the signs and symptoms of a disorder or pathological process" [] -is_a: OBI:0000011 ! planned process +id: OBI:2100007 +name: eosinophil count assay +def: "A cytometry assay that measures the count of eosinophils" [] +is_a: OBI:0003023 ! eosinophil assay [Term] -id: OMIABIS:0000050 -name: fixed tissue specimen -def: "A processed specimen that is the output of a fixation process." [] -is_a: OBI:0000953 ! processed specimen +id: OBI:2100008 +name: lymphocyte count assay +def: "A cytometry assay that measures the count of lymphocytes" [] +is_a: OBI:0003024 ! lymphocyte assay [Term] -id: OMIABIS:0000052 -name: fixed tissue slide specimen -def: "A fixed tissue specimen that is placed in a slide." [] -is_a: OMIABIS:0000050 ! fixed tissue specimen +id: OBI:2100009 +name: monocyte count assay +def: "A cytometry assay that measures the count of monocytes" [] +is_a: OBI:0003025 ! monocyte assay [Term] -id: OMRSE:00000012 -name: health care provider role -def: "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." [] -is_a: BFO:0000023 ! role +id: OBI:2100010 +name: chloride assay +def: "An analyte assay that measures the abundance of chloride" [] +is_a: OBI:0000443 ! analyte assay [Term] -id: ObsoleteClass -name: Obsolete Class +id: OBI:2100011 +name: erythrocyte count assay +def: "A cytometry assay that measures the count of erythrocytes" [] +is_a: OBI:0003018 ! hematocrit assay [Term] -id: PATO:0000011 -name: age -def: "A time quality inhering in a bearer by virtue of how long the bearer has existed." [] -is_a: PATO:0000165 ! time +id: OBI:2100012 +name: platelet count assay +def: "A cytometry assay that measures the count of platelets" [] +is_a: OBI:0003028 ! platelet assay [Term] -id: PATO:0000018 -name: fluorescence -def: "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." [] -is_a: PATO:0001296 ! luminous flux +id: OBI:2100013 +name: leukocyte count assay +def: "A cytometry assay that measures the count of leukocytes" [] +is_a: OBI:0001977 ! cytometry assay [Term] -id: PATO:0000025 -name: composition -def: "A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts." [] -is_a: PATO:0000141 ! structure +id: OBI:2100014 +name: hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin" [] +is_a: OBI:0000443 ! analyte assay [Term] -id: PATO:0000033 -name: concentration of -def: "A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance." [] -is_a: PATO:0002182 ! molecular quality +id: OBI:2100015 +name: phosphate ion assay +def: "An analyte assay that measures the abundance of phosphate ion" [] +is_a: OBI:0000443 ! analyte assay [Term] -id: PATO:0000047 -name: biological sex -def: "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." [] -is_a: PATO:0001995 ! organismal quality +id: OBI:2100016 +name: alanine aminotransferase assay +def: "An analyte assay that measures the abundance of alanine aminotransferase" [] +is_a: OBI:2100023 ! protein assay [Term] -id: PATO:0000051 -name: morphology -def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [] -is_a: PATO:0001241 ! physical object quality +id: OBI:2100017 +name: alkaline phosphatase (human) assay +def: "An analyte assay that measures the abundance of alkaline phosphatase (human)" [] +is_a: OBI:2100023 ! protein assay [Term] -id: PATO:0000117 -name: size -def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [] -is_a: PATO:0000051 ! morphology +id: OBI:2100018 +name: bilirubin IXalpha assay +def: "An analyte assay that measures the abundance of bilirubin IXalpha" [] +is_a: OBI:0000443 ! analyte assay [Term] -id: PATO:0000122 -name: length -def: "A 1-D extent quality which is equal to the distance between two points." [] +id: OBI:2100019 +name: aspartate aminotransferase (human) assay +def: "An analyte assay that measures the abundance of aspartate aminotransferase (human)" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100020 +name: glucose assay +def: "An analyte assay that measures the abundance of glucose" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100021 +name: magnesium cation assay +def: "An analyte assay that measures the abundance of magnesium cation" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100022 +name: albumin assay +def: "An analyte assay that measures the abundance of albumin" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100023 +name: protein assay +def: "An analyte assay that measures the abundance of protein" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100024 +name: calcium cation assay +def: "An analyte assay that measures the abundance of calcium cation" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100025 +name: creatine kinase assay +def: "An analyte assay that measures the abundance of creatine kinase" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100026 +name: nucleate erythrocyte count assay +def: "A cytometry assay that measures the count of nucleate erythrocytes" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100027 +name: segmented neutrophil of bone marrow count assay +def: "A cytometry assay that measures the count of segmented neutrophil of bone marrows" [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:2100028 +name: lactate dehydrogenase complex assay +def: "An assay that measures lactate dehydrogenase complex" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100029 +name: triglyceride assay +def: "An analyte assay that measures the abundance of triglyceride" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100030 +name: high-density lipoprotein cholesterol assay +def: "An analyte assay that measures the abundance of high-density lipoprotein cholesterol" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100031 +name: cholesterol assay +def: "An analyte assay that measures the abundance of cholesterol" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100032 +name: low-density lipoprotein cholesterol assay +def: "An analyte assay that measures the abundance of low-density lipoprotein cholesterol" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100033 +name: thyroid stimulating hormone assay +def: "An analyte assay that measures the abundance of thyroid stimulating hormone" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100034 +name: prostate-specific antigen assay +def: "An analyte assay that measures the abundance of prostate-specific antigen" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100035 +name: thyroxine assay +def: "An analyte assay that measures the abundance of thyroxine" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100036 +name: elemental oxygen assay +def: "An analyte assay that measures the abundance of elemental oxygen" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100037 +name: folic acids assay +def: "An analyte assay that measures the abundance of folic acids" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100038 +name: reticulocyte count assay +def: "A cytometry assay that measures the count of reticulocytes" [] +is_a: OBI:0003026 ! reticulocyte assay + +[Term] +id: OBI:2100039 +name: osmolality assay +def: "An assay that measures osmolality" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100040 +name: methemoglobin assay +def: "An analyte assay that measures the abundance of methemoglobin" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100041 +name: cytosolic creatine kinase complex, MB-type assay +def: "An assay that measures cytosolic creatine kinase complex, MB-type" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100042 +name: rac-lactic acid assay +def: "An assay that measures rac-lactic acid" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100043 +name: hydrogencarbonate assay +def: "An analyte assay that measures the abundance of hydrogencarbonate" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100044 +name: vancomycin assay +def: "An analyte assay that measures the abundance of vancomycin" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100045 +name: tobramycin assay +def: "An analyte assay that measures the abundance of tobramycin" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100046 +name: 3,3',5'-triiodothyronine assay +def: "An analyte assay that measures the abundance of 3,3',5'-triiodothyronine" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100047 +name: C-reactive protein assay +def: "An analyte assay that measures the abundance of C-reactive protein" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100048 +name: megakaryocyte count assay +def: "A cytometry assay that measures the count of megakaryocytes" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100049 +name: mesothelial cell count assay +def: "A cytometry assay that measures the count of mesothelial cells" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100050 +name: macrophage count assay +def: "A cytometry assay that measures the count of macrophages" [] +is_a: OBI:0003027 ! macrophage assay + +[Term] +id: OBI:2100051 +name: 3-hydroxybutyric acid assay +def: "An analyte assay that measures the abundance of 3-hydroxybutyric acid" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100052 +name: panel5 venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100053 +name: panel5 venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100054 +name: panel5 venous blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100055 +name: panel5 venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100056 +name: automated differential venous blood basophil count assay +def: "A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order" [] +is_a: OBI:0003021 ! basophil assay + +[Term] +id: OBI:2100057 +name: automated differential venous blood neutrophil count assay +def: "A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order" [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:2100058 +name: automated differential venous blood eosinophil count assay +def: "A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order" [] +is_a: OBI:0003023 ! eosinophil assay + +[Term] +id: OBI:2100059 +name: automated differential venous blood lymphocyte count assay +def: "A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order" [] +is_a: OBI:0003024 ! lymphocyte assay + +[Term] +id: OBI:2100060 +name: automated differential venous blood monocyte count assay +def: "A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order" [] +is_a: OBI:0003025 ! monocyte assay + +[Term] +id: OBI:2100061 +name: venous blood chloride assay +def: "An analyte assay that measures the abundance of chloride in venous blood" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100062 +name: CBC with automated differential venous blood RBC count assay +def: "A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100063 +name: CBC with automated differential venous blood platelet count assay +def: "A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order" [] +is_a: OBI:0003028 ! platelet assay + +[Term] +id: OBI:2100064 +name: CBC with automated differential venous blood WBC count assay +def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100065 +name: CBC with automated differential venous blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100066 +name: CBC with automated differential venous blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100067 +name: venous blood phosphate assay +def: "An analyte assay that measures the abundance of phosphate in venous blood" [] +is_a: OBI:2100015 ! phosphate ion assay + +[Term] +id: OBI:2100068 +name: liver injury venous blood alanine aminotransferase assay +def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order" [] +is_a: OBI:2100016 ! alanine aminotransferase assay + +[Term] +id: OBI:2100069 +name: liver injury venous blood human alkaline phosphatase assay +def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order" [] +is_a: OBI:2100017 ! alkaline phosphatase (human) assay + +[Term] +id: OBI:2100070 +name: liver injury venous blood bilirubin assay +def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order" [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:2100071 +name: liver injury venous blood human aspartate aminotransferase assay +def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order" [] +is_a: OBI:2100019 ! aspartate aminotransferase (human) assay + +[Term] +id: OBI:2100072 +name: venous blood glucose assay +def: "An analyte assay that measures the abundance of glucose in venous blood" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100073 +name: venous blood magnesium assay +def: "An analyte assay that measures the abundance of magnesium in venous blood" [] +is_a: OBI:2100021 ! magnesium cation assay + +[Term] +id: OBI:2100074 +name: CBC venous blood RBC count assay +def: "A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100075 +name: CBC venous blood WBC count assay +def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100076 +name: CBC venous blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100077 +name: CBC venous blood platelet count assay +def: "A cytometry assay that measures the count of platelets in venous blood as part of a CBC order" [] +is_a: OBI:0003028 ! platelet assay + +[Term] +id: OBI:2100078 +name: CBC venous blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100079 +name: corrected venous blood leukocyte count assay +def: "A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100080 +name: liver evaluation venous blood bilirubin assay +def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order" [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:2100081 +name: liver evaluation venous blood globulin assay +def: "An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order" [] +is_a: OBI:0003015 ! globulin assay + +[Term] +id: OBI:2100082 +name: liver evaluation venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100083 +name: liver evaluation venous blood human aspartate aminotransferase assay +def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order" [] +is_a: OBI:2100019 ! aspartate aminotransferase (human) assay + +[Term] +id: OBI:2100084 +name: liver evaluation venous blood alanine aminotransferase assay +def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order" [] +is_a: OBI:2100016 ! alanine aminotransferase assay + +[Term] +id: OBI:2100085 +name: liver evaluation venous blood human alkaline phosphatase assay +def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order" [] +is_a: OBI:2100017 ! alkaline phosphatase (human) assay + +[Term] +id: OBI:2100086 +name: liver evaluation venous blood protein assay +def: "An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100087 +name: basic metabolic panel venous blood chloride assay +def: "An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100088 +name: basic metabolic panel venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100089 +name: basic metabolic panel venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100090 +name: basic metabolic panel venous blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100091 +name: basic metabolic panel venous blood glucose assay +def: "An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100092 +name: basic metabolic panel venous blood calcium assay +def: "An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100093 +name: basic metabolic panel venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100094 +name: venous blood creatine kinase assay +def: "An analyte assay that measures the abundance of creatine kinase in venous blood" [] +is_a: OBI:2100025 ! creatine kinase assay + +[Term] +id: OBI:2100095 +name: venous blood calcium assay +def: "An analyte assay that measures the abundance of calcium in venous blood" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100096 +name: venous blood ferritin assay +def: "An assay that measures ferritin in venous blood" [] +is_a: OBI:0003009 ! ferritin assay + +[Term] +id: OBI:2100097 +name: total venous blood calcium assay +def: "An analyte assay that measures the abundance of calcium in venous blood as part of a total order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100098 +name: venous blood iron assay +def: "An analyte assay that measures the abundance of iron in venous blood" [] +is_a: OBI:0003011 ! iron assay + +[Term] +id: OBI:2100099 +name: CBC with manual differential venous blood band neutrophil count assay +def: "A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:2100100 +name: CBC with manual differential venous blood WBC count assay +def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100101 +name: CBC with manual differential venous blood eosinophil count assay +def: "A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003023 ! eosinophil assay + +[Term] +id: OBI:2100102 +name: CBC with manual differential venous blood lymphocyte count assay +def: "A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003024 ! lymphocyte assay + +[Term] +id: OBI:2100103 +name: CBC with manual differential venous blood nucleated RBC count assay +def: "A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100104 +name: CBC with manual differential venous blood monocyte count assay +def: "A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003025 ! monocyte assay + +[Term] +id: OBI:2100105 +name: CBC with manual differential venous blood segmented neutrophil count assay +def: "A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:2100106 +name: CBC with manual differential venous blood basophil count assay +def: "A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003021 ! basophil assay + +[Term] +id: OBI:2100107 +name: venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100108 +name: cardiac enzymes venous blood creatine kinase assay +def: "An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order" [] +is_a: OBI:2100025 ! creatine kinase assay + +[Term] +id: OBI:2100109 +name: venous blood haptoglobin assay +def: "An analyte assay that measures the abundance of haptoglobin in venous blood" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100110 +name: venous blood lactate dehydrogenase assay +def: "An assay that measures lactate dehydrogenase in venous blood" [] +is_a: OBI:2100028 ! lactate dehydrogenase complex assay + +[Term] +id: OBI:2100111 +name: venous blood prealbunin assay +def: "An analyte assay that measures the abundance of prealbunin in venous blood" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100112 +name: lipid panel venous blood triglyceride assay +def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order" [] +is_a: OBI:2100029 ! triglyceride assay + +[Term] +id: OBI:2100113 +name: lipid panel venous blood high density lipoprotein assay +def: "An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order" [] +is_a: OBI:2100030 ! high-density lipoprotein cholesterol assay + +[Term] +id: OBI:2100114 +name: lipid panel venous blood cholesterol assay +def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order" [] +is_a: OBI:2100031 ! cholesterol assay + +[Term] +id: OBI:2100115 +name: lipid panel venous blood low density lipoprotein assay +def: "An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order" [] +is_a: OBI:2100032 ! low-density lipoprotein cholesterol assay + +[Term] +id: OBI:2100116 +name: venous blood hemoglobin A1c assay +def: "An assay that measures hemoglobin A1c in venous blood" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100117 +name: venous blood uric acid assay +def: "An analyte assay that measures the abundance of uric acid in venous blood" [] +is_a: OBI:0003014 ! uric acid assay + +[Term] +id: OBI:2100118 +name: total venous blood protein assay +def: "An analyte assay that measures the abundance of protein in venous blood as part of a total order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100119 +name: venous blood thyroid stimulating hormone assay +def: "An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood" [] +is_a: OBI:2100033 ! thyroid stimulating hormone assay + +[Term] +id: OBI:2100120 +name: venous blood prostate specific antigen assay +def: "An analyte assay that measures the abundance of prostate specific antigen in venous blood" [] +is_a: OBI:2100034 ! prostate-specific antigen assay + +[Term] +id: OBI:2100121 +name: 24 hour total urine volume assay +def: "An assay that measures volume in urine as part of a 24 hour total order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100122 +name: T4 uptake venous blood T4 assay +def: "An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order" [] +is_a: OBI:2100035 ! thyroxine assay + +[Term] +id: OBI:2100123 +name: arterial blood glucose assay +def: "An analyte assay that measures the abundance of glucose in arterial blood" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100124 +name: CBC with manual differential venous blood cell count assay +def: "A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100125 +name: hemoglobin oxygen saturation arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100126 +name: hemoglobin oxygen saturation arterial blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100127 +name: inpatient profile venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100128 +name: inpatient profile venous blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100129 +name: inpatient profile venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100130 +name: inpatient profile venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100131 +name: venous blood folic acid assay +def: "An analyte assay that measures the abundance of folic acid in venous blood" [] +is_a: OBI:2100037 ! folic acids assay + +[Term] +id: OBI:2100132 +name: count venous blood reticulocyte count assay +def: "A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order" [] +is_a: OBI:0003026 ! reticulocyte assay + +[Term] +id: OBI:2100133 +name: venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100134 +name: venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100135 +name: venous blood transferrin assay +def: "An analyte assay that measures the abundance of transferrin in venous blood" [] +is_a: OBI:0003013 ! transferrin assay + +[Term] +id: OBI:2100136 +name: venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100137 +name: random electrolytes urine sodium assay +def: "An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100138 +name: random electrolytes urine potassium assay +def: "An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100139 +name: urine creatinine assay +def: "An analyte assay that measures the abundance of creatinine in urine" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100140 +name: urine osmolality assay +def: "An assay that measures osmolality in urine" [] +is_a: OBI:2100039 ! osmolality assay + +[Term] +id: OBI:2100141 +name: cooximitery arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100142 +name: cooximitery arterial blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100143 +name: cooximitery arterial blood methemoglobin assay +def: "An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order" [] +is_a: OBI:2100040 ! methemoglobin assay + +[Term] +id: OBI:2100144 +name: electrolytes urine sodium assay +def: "An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100145 +name: electrolytes urine potassium assay +def: "An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100146 +name: Biosite cardiac panel arterial blood creatine kinase MB assay +def: "An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order" [] +is_a: OBI:2100041 ! cytosolic creatine kinase complex, MB-type assay + +[Term] +id: OBI:2100147 +name: venous blood fibrinogen assay +def: "An assay that measures fibrinogen in venous blood" [] +is_a: OBI:0003010 ! fibrinogen assay + +[Term] +id: OBI:2100148 +name: comprehensive metabolic panel venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100149 +name: comprehensive metabolic panel venous blood calcium assay +def: "An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100150 +name: comprehensive metabolic panel venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100151 +name: comprehensive metabolic panel venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100152 +name: comprehensive metabolic panel venous blood glucose assay +def: "An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100153 +name: comprehensive metabolic panel venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100154 +name: comprehensive metabolic panel venous blood human alkaline phosphatase assay +def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100017 ! alkaline phosphatase (human) assay + +[Term] +id: OBI:2100155 +name: comprehensive metabolic panel venous blood bilirubin assay +def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:2100156 +name: comprehensive metabolic panel venous blood chloride assay +def: "An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100157 +name: comprehensive metabolic panel venous blood human aspartate aminotransferase assay +def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100019 ! aspartate aminotransferase (human) assay + +[Term] +id: OBI:2100158 +name: comprehensive metabolic panel venous blood protein assay +def: "An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100159 +name: comprehensive metabolic panel venous blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100160 +name: comprehensive metabolic panel venous blood alanine aminotransferase assay +def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order" [] +is_a: OBI:2100016 ! alanine aminotransferase assay + +[Term] +id: OBI:2100161 +name: venous blood LDH assay +def: "An assay that measures LDH in venous blood" [] +is_a: OBI:2100028 ! lactate dehydrogenase complex assay + +[Term] +id: OBI:2100162 +name: venous blood creatine kinase MB assay +def: "An assay that measures creatine kinase MB in venous blood" [] +is_a: OBI:2100041 ! cytosolic creatine kinase complex, MB-type assay + +[Term] +id: OBI:2100163 +name: venous blood lactic acid assay +def: "An assay that measures lactic acid in venous blood" [] +is_a: OBI:2100042 ! rac-lactic acid assay + +[Term] +id: OBI:2100164 +name: venous blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in venous blood" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100165 +name: venous blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in venous blood" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100166 +name: blood gas venous blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100167 +name: ionized venous blood ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100168 +name: blood gas venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100169 +name: blood gas venous blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100170 +name: arterial blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in arterial blood" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100171 +name: venous blood tacrolimus assay +def: "An analyte assay that measures the abundance of tacrolimus in venous blood" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100172 +name: random venous blood vancomycin assay +def: "An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order" [] +is_a: OBI:2100044 ! vancomycin assay + +[Term] +id: OBI:2100173 +name: venous blood mycophenolic acid assay +def: "An analyte assay that measures the abundance of mycophenolic acid in venous blood" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100174 +name: non-vented blood gas arterial blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100175 +name: non-vented blood gas arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100176 +name: non-vented blood gas arterial blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100177 +name: quantitative venous blood IgG assay +def: "An assay that measures IgG in venous blood as part of a quantitative order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100178 +name: quantitative venous blood IgM assay +def: "An assay that measures IgM in venous blood as part of a quantitative order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100179 +name: quantitative venous blood IgA assay +def: "An assay that measures IgA in venous blood as part of a quantitative order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100180 +name: arterial blood sodium assay +def: "An analyte assay that measures the abundance of sodium in arterial blood" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100181 +name: arterial blood potassium assay +def: "An analyte assay that measures the abundance of potassium in arterial blood" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100182 +name: ionized arterial blood calcium assay +def: "An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100183 +name: vented blood gas arterial blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100184 +name: vented blood gas arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100185 +name: vented blood gas arterial blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100186 +name: arterial blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in arterial blood" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100187 +name: arterial blood chloride assay +def: "An analyte assay that measures the abundance of chloride in arterial blood" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100188 +name: arterial blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in arterial blood" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100189 +name: GEM premier blood gas venous blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100190 +name: GEM premier blood gas venous blood ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100191 +name: GEM premier blood gas venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100192 +name: GEM premier blood gas venous blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100193 +name: GEM premier blood gas venous blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100194 +name: GEM premier blood gas venous blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100195 +name: GEM premier blood gas venous blood glucose assay +def: "An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100196 +name: GEM premier blood gas venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100197 +name: GEM premier blood gas venous blood lactic acid assay +def: "An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:2100042 ! rac-lactic acid assay + +[Term] +id: OBI:2100198 +name: GEM premier blood gas venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100199 +name: trough venous blood tobramycin assay +def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order" [] +is_a: OBI:2100045 ! tobramycin assay + +[Term] +id: OBI:2100200 +name: random venous blood tobramycin assay +def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order" [] +is_a: OBI:2100045 ! tobramycin assay + +[Term] +id: OBI:2100201 +name: CBC with manual differential venous blood metamyelocyte count assay +def: "A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003017 ! metamyelocyte assay + +[Term] +id: OBI:2100202 +name: arterial blood lactic acid assay +def: "An assay that measures lactic acid in arterial blood" [] +is_a: OBI:2100042 ! rac-lactic acid assay + +[Term] +id: OBI:2100203 +name: venous blood 25-hydroxyvitamin D2 assay +def: "An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100204 +name: venous blood digoxin assay +def: "An analyte assay that measures the abundance of digoxin in venous blood" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100205 +name: urine protein assay +def: "An analyte assay that measures the abundance of protein in urine" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100206 +name: venous blood tobramycin assay +def: "An analyte assay that measures the abundance of tobramycin in venous blood" [] +is_a: OBI:2100045 ! tobramycin assay + +[Term] +id: OBI:2100207 +name: CBC with manual differential venous blood myelocyte count assay +def: "A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003016 ! myelocyte assay + +[Term] +id: OBI:2100208 +name: SPEP protein electrophoresis venous blood beta-globin assay +def: "An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100209 +name: SPEP protein electrophoresis venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100210 +name: SPEP protein electrophoresis venous blood protein assay +def: "An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100211 +name: trough venous blood vancomycin assay +def: "An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order" [] +is_a: OBI:2100044 ! vancomycin assay + +[Term] +id: OBI:2100212 +name: hepatic panel venous blood protein assay +def: "An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100213 +name: hepatic panel venous blood bilirubin assay +def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order" [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:2100214 +name: hepatic panel venous blood alanine aminotransferase assay +def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order" [] +is_a: OBI:2100016 ! alanine aminotransferase assay + +[Term] +id: OBI:2100215 +name: hepatic panel venous blood human aspartate aminotransferase assay +def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order" [] +is_a: OBI:2100019 ! aspartate aminotransferase (human) assay + +[Term] +id: OBI:2100216 +name: hepatic panel venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100217 +name: hepatic panel venous blood human alkaline phosphatase assay +def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order" [] +is_a: OBI:2100017 ! alkaline phosphatase (human) assay + +[Term] +id: OBI:2100218 +name: estimated venous blood glomerular filtration assay +def: "An assay that measures glomerular filtration in venous blood as part of a estimated order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100219 +name: DT60 venous blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100220 +name: fasting venous blood glucose assay +def: "An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100221 +name: random venous blood amikacin assay +def: "An analyte assay that measures the abundance of amikacin in venous blood as part of a random order" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100222 +name: venous blood ammonia assay +def: "An analyte assay that measures the abundance of ammonia in venous blood" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100223 +name: venous blood GGT assay +def: "An analyte assay that measures the abundance of GGT in venous blood" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100224 +name: chem11 venous blood phosphate assay +def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order" [] +is_a: OBI:2100015 ! phosphate ion assay + +[Term] +id: OBI:2100225 +name: chem11 venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100226 +name: chem11 venous blood calcium assay +def: "An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100227 +name: chem11 venous blood glucose assay +def: "An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100228 +name: chem11 venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100229 +name: chem11 venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100230 +name: chem11 venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100231 +name: chem11 venous blood magnesium assay +def: "An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order" [] +is_a: OBI:2100021 ! magnesium cation assay + +[Term] +id: OBI:2100232 +name: chem11 venous blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100233 +name: chem11 venous blood chloride assay +def: "An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100234 +name: total venous blood IgE assay +def: "An assay that measures IgE in venous blood as part of a total order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100235 +name: chem16 venous blood human aspartate aminotransferase assay +def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order" [] +is_a: OBI:2100019 ! aspartate aminotransferase (human) assay + +[Term] +id: OBI:2100236 +name: chem16 venous blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100237 +name: chem16 venous blood magnesium assay +def: "An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order" [] +is_a: OBI:2100021 ! magnesium cation assay + +[Term] +id: OBI:2100238 +name: chem16 venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100239 +name: chem16 venous blood glucose assay +def: "An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100240 +name: chem16 venous blood calcium assay +def: "An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100241 +name: chem16 venous blood triglyceride assay +def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order" [] +is_a: OBI:2100029 ! triglyceride assay + +[Term] +id: OBI:2100242 +name: chem16 venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100243 +name: chem16 venous blood phosphate assay +def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order" [] +is_a: OBI:2100015 ! phosphate ion assay + +[Term] +id: OBI:2100244 +name: chem16 venous blood human alkaline phosphatase assay +def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order" [] +is_a: OBI:2100017 ! alkaline phosphatase (human) assay + +[Term] +id: OBI:2100245 +name: chem16 venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100246 +name: chem16 venous blood bilirubin assay +def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order" [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:2100247 +name: chem16 venous blood chloride assay +def: "An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100248 +name: chem16 venous blood alanine aminotransferase assay +def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order" [] +is_a: OBI:2100016 ! alanine aminotransferase assay + +[Term] +id: OBI:2100249 +name: chem16 venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100250 +name: POC chem8 arterial blood glucose assay +def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100251 +name: POC chem8 arterial blood ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100252 +name: POC chem8 arterial blood potassium assay +def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100253 +name: POC chem8 arterial blood sodium assay +def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100254 +name: POC chem8 arterial blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100255 +name: POC chem8 arterial blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100256 +name: POC chem8 arterial blood chloride assay +def: "An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100257 +name: peak venous blood tobramycin assay +def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order" [] +is_a: OBI:2100045 ! tobramycin assay + +[Term] +id: OBI:2100258 +name: 24 hour urine creatinine assay +def: "An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100259 +name: intact venous blood PTH assay +def: "An analyte assay that measures the abundance of PTH in venous blood as part of a intact order" [] +is_a: OBI:2100034 ! prostate-specific antigen assay + +[Term] +id: OBI:2100260 +name: total venous blood PSA assay +def: "An analyte assay that measures the abundance of PSA in venous blood as part of a total order" [] +is_a: OBI:2100034 ! prostate-specific antigen assay + +[Term] +id: OBI:2100261 +name: total venous blood T3 assay +def: "An analyte assay that measures the abundance of T3 in venous blood as part of a total order" [] +is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay + +[Term] +id: OBI:2100262 +name: 24 hour urine protein assay +def: "An analyte assay that measures the abundance of protein in urine as part of a 24 hour order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100263 +name: total venous blood cholesterol assay +def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order" [] +is_a: OBI:2100031 ! cholesterol assay + +[Term] +id: OBI:2100264 +name: venous blood triglyceride assay +def: "An analyte assay that measures the abundance of triglyceride in venous blood" [] +is_a: OBI:2100029 ! triglyceride assay + +[Term] +id: OBI:2100265 +name: tube 4 count cerebrospinal fluid cell count assay +def: "A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100266 +name: cerebrospinal fluid protein assay +def: "An analyte assay that measures the abundance of protein in cerebrospinal fluid" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100267 +name: cerebrospinal fluid glucose assay +def: "An analyte assay that measures the abundance of glucose in cerebrospinal fluid" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100268 +name: tube 1 count cerebrospinal fluid cell count assay +def: "A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100269 +name: venous blood dehydroepiandrosterone assay +def: "An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100270 +name: venous blood cortisol assay +def: "An analyte assay that measures the abundance of cortisol in venous blood" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100271 +name: ABL90 panel arterial blood sodium assay +def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100272 +name: ABL90 panel arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100273 +name: ABL90 panel arterial blood glucose assay +def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100274 +name: ABL90 panel arterial blood lactic acid assay +def: "An assay that measures lactic acid in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100042 ! rac-lactic acid assay + +[Term] +id: OBI:2100275 +name: ABL90 panel arterial blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100276 +name: ABL90 panel arterial blood chloride assay +def: "An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100277 +name: ABL90 panel arterial blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100278 +name: ABL90 panel arterial blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100279 +name: ABL90 panel arterial blood calcium assay +def: "An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100280 +name: ABL90 panel arterial blood temperature assay +def: "An assay that measures temperature in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100281 +name: ABL90 panel arterial blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100282 +name: ABL90 panel arterial blood potassium assay +def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100283 +name: CBC with manual differential venous blood promyelocyte count assay +def: "A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003019 ! promyelocyte assay + +[Term] +id: OBI:2100284 +name: ABL90 panel venous blood glucose assay +def: "An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100285 +name: ABL90 panel venous blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100286 +name: ABL90 panel venous blood ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100287 +name: ABL90 panel venous blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100288 +name: ABL90 panel venous blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100289 +name: ABL90 panel venous blood sodium assay +def: "An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100290 +name: ABL90 panel venous blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100291 +name: ABL90 panel venous blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100292 +name: ABL90 panel venous blood lactic acid assay +def: "An assay that measures lactic acid in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100042 ! rac-lactic acid assay + +[Term] +id: OBI:2100293 +name: ABL90 panel venous blood chloride assay +def: "An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100010 ! chloride assay + +[Term] +id: OBI:2100294 +name: venous blood T4 assay +def: "An analyte assay that measures the abundance of T4 in venous blood" [] +is_a: OBI:2100035 ! thyroxine assay + +[Term] +id: OBI:2100295 +name: free venous blood T4 assay +def: "An analyte assay that measures the abundance of T4 in venous blood as part of a free order" [] +is_a: OBI:2100035 ! thyroxine assay + +[Term] +id: OBI:2100296 +name: ABL90 panel venous blood potassium assay +def: "An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100297 +name: urine sodium assay +def: "An analyte assay that measures the abundance of sodium in urine" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100298 +name: bone profile venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100299 +name: bone profile venous blood calcium assay +def: "An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100300 +name: bone profile venous blood human alkaline phosphatase assay +def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order" [] +is_a: OBI:2100017 ! alkaline phosphatase (human) assay + +[Term] +id: OBI:2100301 +name: bone profile venous blood protein assay +def: "An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100302 +name: bone profile venous blood phosphate assay +def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order" [] +is_a: OBI:2100015 ! phosphate ion assay + +[Term] +id: OBI:2100303 +name: ABG/electrolytes arterial blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100304 +name: ABG/electrolytes arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100305 +name: ABG/electrolytes arterial blood ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100306 +name: CBC with automated differential venous blood nucleated RBC count assay +def: "A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100307 +name: ABL90 panel venous blood methemoglobin assay +def: "An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order" [] +is_a: OBI:2100040 ! methemoglobin assay + +[Term] +id: OBI:2100308 +name: ABL90 panel arterial blood methemoglobin assay +def: "An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order" [] +is_a: OBI:2100040 ! methemoglobin assay + +[Term] +id: OBI:2100309 +name: venous blood valproic acid assay +def: "An analyte assay that measures the abundance of valproic acid in venous blood" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100310 +name: high sensitivity cardiac/neonatal venous blood c-reactive protein assay +def: "An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order" [] +is_a: OBI:2100047 ! C-reactive protein assay + +[Term] +id: OBI:2100311 +name: POC arterial blood creatinine assay +def: "An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100312 +name: GEM4000 ANLCOOX arterial blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100313 +name: GEM4000 ANLCOOX arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100314 +name: GEM4000 ANLCOOX arterial blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100315 +name: GEM4000 ANLCOOX arterial blood temperature assay +def: "An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100316 +name: GEM4000 ANLCOOX arterial blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100317 +name: GEM4000 ANLCOOX arterial blood potassium assay +def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100318 +name: GEM4000 ANLCOOX arterial blood glucose assay +def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100319 +name: GEM4000 ANLCOOX arterial blood ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100320 +name: GEM4000 ANLCOOX arterial blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100321 +name: GEM4000 ANLCOOX arterial blood sodium assay +def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100322 +name: ionized venous blood calcium assay +def: "An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100323 +name: venous blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in venous blood" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100324 +name: CBC with manual differential venous blood megakaryocyte count assay +def: "A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100325 +name: non-cardiac venous blood c-reactive protein assay +def: "An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order" [] +is_a: OBI:2100047 ! C-reactive protein assay + +[Term] +id: OBI:2100326 +name: intraoperative venous blood PTH assay +def: "An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order" [] +is_a: OBI:2100034 ! prostate-specific antigen assay + +[Term] +id: OBI:2100327 +name: venous blood parathyroid hormone assay +def: "An analyte assay that measures the abundance of parathyroid hormone in venous blood" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100328 +name: total bodily fluid protein assay +def: "An analyte assay that measures the abundance of protein in bodily fluid as part of a total order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100329 +name: bodily fluid glucose assay +def: "An analyte assay that measures the abundance of glucose in bodily fluid" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100330 +name: count bodily fluid cell count assay +def: "A cytometry assay that measures the count of cells in bodily fluid as part of a count order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100331 +name: manual differential bodily fluid segmented neutrophil count assay +def: "A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order" [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:2100332 +name: manual differential bodily fluid mesothelial cell count assay +def: "A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100333 +name: manual differential bodily fluid monocyte count assay +def: "A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order" [] +is_a: OBI:0003025 ! monocyte assay + +[Term] +id: OBI:2100334 +name: manual differential bodily fluid lymphocyte count assay +def: "A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order" [] +is_a: OBI:0003024 ! lymphocyte assay + +[Term] +id: OBI:2100335 +name: manual differential bodily fluid macrophage count assay +def: "A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order" [] +is_a: OBI:0003027 ! macrophage assay + +[Term] +id: OBI:2100336 +name: manual differential bodily fluid basophil count assay +def: "A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order" [] +is_a: OBI:0003021 ! basophil assay + +[Term] +id: OBI:2100337 +name: manual differential bodily fluid eosinophil count assay +def: "A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order" [] +is_a: OBI:0003023 ! eosinophil assay + +[Term] +id: OBI:2100338 +name: liver function venous blood bilirubin assay +def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order" [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:2100339 +name: liver function venous blood alanine aminotransferase assay +def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order" [] +is_a: OBI:2100016 ! alanine aminotransferase assay + +[Term] +id: OBI:2100340 +name: liver function venous blood human aspartate aminotransferase assay +def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order" [] +is_a: OBI:2100019 ! aspartate aminotransferase (human) assay + +[Term] +id: OBI:2100341 +name: liver function venous blood albumin assay +def: "An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100342 +name: liver function venous blood protein assay +def: "An analyte assay that measures the abundance of protein in venous blood as part of a liver function order" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100343 +name: liver function venous blood human alkaline phosphatase assay +def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order" [] +is_a: OBI:2100017 ! alkaline phosphatase (human) assay + +[Term] +id: OBI:2100344 +name: vitamin B12 and Folate venous blood folic acid assay +def: "An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order" [] +is_a: OBI:2100037 ! folic acids assay + +[Term] +id: OBI:2100345 +name: bodily fluid cell count assay +def: "A cytometry assay that measures the count of cells in bodily fluid" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100346 +name: venous blood reticulocyte count assay +def: "A cytometry assay that measures the count of reticulocytes in venous blood" [] +is_a: OBI:0003026 ! reticulocyte assay + +[Term] +id: OBI:2100347 +name: bodily fluid cholesterol assay +def: "An analyte assay that measures the abundance of cholesterol in bodily fluid" [] +is_a: OBI:2100031 ! cholesterol assay + +[Term] +id: OBI:2100348 +name: TSH reflex Free T4 venous blood thyroid stimulating hormone assay +def: "An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order" [] +is_a: OBI:2100033 ! thyroid stimulating hormone assay + +[Term] +id: OBI:2100349 +name: direct venous blood bilirubin assay +def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order" [] +is_a: OBI:2100018 ! bilirubin IXalpha assay + +[Term] +id: OBI:2100350 +name: free venous blood T3 assay +def: "An analyte assay that measures the abundance of T3 in venous blood as part of a free order" [] +is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay + +[Term] +id: OBI:2100351 +name: bodily fluid albumin assay +def: "An analyte assay that measures the abundance of albumin in bodily fluid" [] +is_a: OBI:2100022 ! albumin assay + +[Term] +id: OBI:2100352 +name: bodily fluid triglyceride assay +def: "An analyte assay that measures the abundance of triglyceride in bodily fluid" [] +is_a: OBI:2100029 ! triglyceride assay + +[Term] +id: OBI:2100353 +name: hemoglobin and hematocrit venous blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100354 +name: hemoglobin and hematocrit venous blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100355 +name: venous blood ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium in venous blood" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100356 +name: venous blood temperature assay +def: "An assay that measures temperature in venous blood" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100357 +name: venous blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in venous blood" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100358 +name: venous blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in venous blood" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100359 +name: venous blood osmolality assay +def: "An assay that measures osmolality in venous blood" [] +is_a: OBI:2100039 ! osmolality assay + +[Term] +id: OBI:2100360 +name: liver fibrosis (chronic viral hepatitis) venous blood platelet count assay +def: "A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order" [] +is_a: OBI:0003028 ! platelet assay + +[Term] +id: OBI:2100361 +name: venous blood T3 assay +def: "An analyte assay that measures the abundance of T3 in venous blood" [] +is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay + +[Term] +id: OBI:2100362 +name: CBC with manual differential venous blood neutrophil count assay +def: "A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:2100363 +name: creatinine clearance urine creatinine assay +def: "An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order" [] +is_a: OBI:2100003 ! creatinine assay + +[Term] +id: OBI:2100364 +name: venous blood beta hydroxybutryic acid assay +def: "An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood" [] +is_a: OBI:2100051 ! 3-hydroxybutyric acid assay + +[Term] +id: OBI:2100365 +name: venous blood megakaryocyte count assay +def: "A cytometry assay that measures the count of megakaryocytes in venous blood" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100366 +name: venous blood nucleated RBC count assay +def: "A cytometry assay that measures the count of nucleated RBCs in venous blood" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100367 +name: venous blood WBC count assay +def: "A cytometry assay that measures the count of WBCs in venous blood" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100368 +name: automated count venous blood reticulocyte count assay +def: "A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order" [] +is_a: OBI:0003026 ! reticulocyte assay + +[Term] +id: OBI:2100369 +name: total venous blood homocysteine assay +def: "An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order" [] +is_a: OBI:0000443 ! analyte assay + +[Term] +id: OBI:2100370 +name: venous blood Ceruloplasmin assay +def: "An analyte assay that measures the abundance of Ceruloplasmin in venous blood" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100371 +name: GEM4 arterial blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100372 +name: GEM4 arterial blood lactic acid assay +def: "An assay that measures lactic acid in arterial blood as part of a GEM4 order" [] +is_a: OBI:2100042 ! rac-lactic acid assay + +[Term] +id: OBI:2100373 +name: GEM4 arterial blood hemoglobin assay +def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order" [] +is_a: OBI:2100014 ! hemoglobin assay + +[Term] +id: OBI:2100374 +name: GEM4 arterial blood sodium assay +def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order" [] +is_a: OBI:2100002 ! sodium(1+) assay + +[Term] +id: OBI:2100375 +name: GEM4 arterial blood potassium assay +def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order" [] +is_a: OBI:2100004 ! potassium(1+) assay + +[Term] +id: OBI:2100376 +name: GEM4 arterial blood temperature assay +def: "An assay that measures temperature in arterial blood as part of a GEM4 order" [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:2100377 +name: GEM4 arterial blood glucose assay +def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order" [] +is_a: OBI:2100020 ! glucose assay + +[Term] +id: OBI:2100378 +name: GEM4 arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100379 +name: GEM4 arterial blood hematocrit assay +def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003018 ! hematocrit assay + +[Term] +id: OBI:2100380 +name: GEM4 arterial blood ionized calcium assay +def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order" [] +is_a: OBI:0003012 ! ionized calcium assay +is_a: OBI:2100024 ! calcium cation assay + +[Term] +id: OBI:2100381 +name: GEM4 arterial blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100382 +name: liver fibrosis (NAFLD) venous blood platelet count assay +def: "A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order" [] +is_a: OBI:0003028 ! platelet assay + +[Term] +id: OBI:2100383 +name: venous blood beta hydroxybutric acid assay +def: "An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood" [] +is_a: OBI:2100051 ! 3-hydroxybutyric acid assay + +[Term] +id: OBI:2100384 +name: CBC with manual differential venous blood plasma cell count assay +def: "A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order" [] +is_a: OBI:0003024 ! lymphocyte assay + +[Term] +id: OBI:2100385 +name: venous blood erythropoietin assay +def: "An analyte assay that measures the abundance of erythropoietin in venous blood" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100386 +name: blood gas arterial blood oxygen assay +def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order" [] +is_a: OBI:2100036 ! elemental oxygen assay + +[Term] +id: OBI:2100387 +name: blood gas arterial blood bicarbonate assay +def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order" [] +is_a: OBI:2100043 ! hydrogencarbonate assay + +[Term] +id: OBI:2100388 +name: blood gas arterial blood carbon dioxide assay +def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order" [] +is_a: OBI:2100001 ! carbon dioxide assay + +[Term] +id: OBI:2100389 +name: free/total venous blood PSA assay +def: "An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order" [] +is_a: OBI:2100034 ! prostate-specific antigen assay + +[Term] +id: OBI:2100390 +name: cerebrospinal fluid lymphocyte count assay +def: "A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid" [] +is_a: OBI:0003024 ! lymphocyte assay + +[Term] +id: OBI:2100391 +name: cerebrospinal fluid segmented neutrophil count assay +def: "A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid" [] +is_a: OBI:0003022 ! neutrophil assay + +[Term] +id: OBI:2100392 +name: cerebrospinal fluid mesothelial cell count assay +def: "A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid" [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:2100393 +name: cerebrospinal fluid macrophage count assay +def: "A cytometry assay that measures the count of macrophages in cerebrospinal fluid" [] +is_a: OBI:0003027 ! macrophage assay + +[Term] +id: OBI:2100394 +name: cerebrospinal fluid basophil count assay +def: "A cytometry assay that measures the count of basophils in cerebrospinal fluid" [] +is_a: OBI:0003021 ! basophil assay + +[Term] +id: OBI:2100395 +name: cerebrospinal fluid monocyte count assay +def: "A cytometry assay that measures the count of monocytes in cerebrospinal fluid" [] +is_a: OBI:0003025 ! monocyte assay + +[Term] +id: OBI:2100396 +name: cerebrospinal fluid eosinophil count assay +def: "A cytometry assay that measures the count of eosinophils in cerebrospinal fluid" [] +is_a: OBI:0003023 ! eosinophil assay + +[Term] +id: OBI:2100397 +name: venous blood beta-2-microglobulin assay +def: "An analyte assay that measures the abundance of beta-2-microglobulin in venous blood" [] +is_a: OBI:2100023 ! protein assay + +[Term] +id: OBI:2100398 +name: lipid panel reflex direct venous blood low density lipoprotein assay +def: "An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order" [] +is_a: OBI:2100032 ! low-density lipoprotein cholesterol assay + +[Term] +id: OBI:2100399 +name: lipid panel reflex direct venous blood triglyceride assay +def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order" [] +is_a: OBI:2100029 ! triglyceride assay + +[Term] +id: OBI:2100400 +name: lipid panel reflex direct venous blood cholesterol assay +def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order" [] +is_a: OBI:2100031 ! cholesterol assay + +[Term] +id: OBI:2100401 +name: lipid panel reflex direct venous blood high density lipoprotein assay +def: "An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order" [] +is_a: OBI:2100030 ! high-density lipoprotein cholesterol assay + +[Term] +id: OBI:9999994 +name: chromium release assay +def: "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." [] +is_a: OBI:0000903 ! in vitro cell killing assay + +[Term] +id: OGMS:0000015 +name: clinical history +def: "A series of statements representing health-relevant qualities of a patient and of a patient's family." [] +is_a: IAO:0000030 ! information content entity + +[Term] +id: OGMS:0000023 +name: phenotype +def: "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." [] +is_a: BFO:0000019 ! quality + +[Term] +id: OGMS:0000031 +name: disease +def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] +is_a: BFO:0000016 ! disposition + +[Term] +id: OGMS:0000063 +name: disease course +def: "The totality of all processes through which a given disease instance is realized." [] +is_a: GO:0008150 ! biological_process + +[Term] +id: OGMS:0000073 +name: diagnosis +def: "The representation of a conclusion of a diagnostic process." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OGMS:0000090 +name: treatment +def: "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" [] +is_a: OBI:0000011 ! planned process + +[Term] +id: OMIABIS:0000050 +name: fixed tissue specimen +def: "A processed specimen that is the output of a fixation process." [] +is_a: OBI:0000953 ! processed specimen + +[Term] +id: OMIABIS:0000052 +name: fixed tissue slide specimen +def: "A fixed tissue specimen that is placed in a slide." [] +is_a: OMIABIS:0000050 ! fixed tissue specimen + +[Term] +id: OMRSE:00000012 +name: health care provider role +def: "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." [] +is_a: BFO:0000023 ! role + +[Term] +id: ObsoleteClass +name: Obsolete Class + +[Term] +id: PATO:0000011 +name: age +def: "A time quality inhering in a bearer by virtue of how long the bearer has existed." [] +is_a: PATO:0000165 ! time + +[Term] +id: PATO:0000018 +name: fluorescence +def: "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." [] +is_a: PATO:0001296 ! luminous flux + +[Term] +id: PATO:0000025 +name: composition +def: "A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts." [] +is_a: PATO:0000141 ! structure + +[Term] +id: PATO:0000033 +name: concentration of +def: "A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance." [] +is_a: PATO:0002182 ! molecular quality + +[Term] +id: PATO:0000047 +name: biological sex +def: "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." [] +is_a: PATO:0001995 ! organismal quality + +[Term] +id: PATO:0000051 +name: morphology +def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [] +is_a: PATO:0001241 ! physical object quality + +[Term] +id: PATO:0000117 +name: size +def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [] +is_a: PATO:0000051 ! morphology + +[Term] +id: PATO:0000122 +name: length +def: "A 1-D extent quality which is equal to the distance between two points." [] is_a: PATO:0000051 ! morphology [Term] @@ -23549,6 +26910,12 @@ name: population quality def: "A quality that inheres in an entire population or part of a population." [] is_a: PATO:0001241 ! physical object quality +[Term] +id: PATO:0002027 +name: osmolality +def: "A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent." [] +is_a: PATO:0000033 ! concentration of + [Term] id: PATO:0002182 name: molecular quality @@ -23609,6 +26976,12 @@ name: CD3 subunit with immunoglobulin domain def: "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." [] is_a: PR:000000001 ! protein +[Term] +id: PR:000003015 +name: prostate-specific antigen +def: "A protein that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + [Term] id: PR:000003252 name: antithrombin-III @@ -23621,24 +26994,84 @@ name: double-stranded RNA-specific adenosine deaminase def: "A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein +[Term] +id: PR:000003918 +name: albumin +def: "A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000004580 +name: beta-2-microglobulin +def: "A protein that is a translation product of the human B2M gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000005794 +name: ceruloplasmin +def: "A protein that is a translation product of the human CP gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000005897 +name: C-reactive protein +def: "A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + [Term] id: PR:000006592 name: deoxyribonuclease-1 def: "A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein +[Term] +id: PR:000007141 +name: erythropoietin +def: "A protein that is a translation product of the human EPO gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + [Term] id: PR:000007928 name: glial cell line-derived neurotrophic factor def: "A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein +[Term] +id: PR:000008457 +name: beta-globin +def: "A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000008725 +name: haptoglobin +def: "A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000013429 +name: parathyroid hormone +def: "A protein that is a translation product of the human PTH gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + [Term] id: PR:000014060 name: ribonuclease T2 def: "A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein +[Term] +id: PR:000016261 +name: serotransferrin +def: "A protein that is a translation product of the human TF gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000016801 +name: transthyretin +def: "A protein that is a translation product of the human TTR gene or a 1:1 ortholog thereof." [] +is_a: PR:000000001 ! protein + [Term] id: PR:000023089 name: DNA ligase @@ -23650,7 +27083,7 @@ is_a: PR:000000001 ! protein [Term] id: PR:000025402 name: T cell receptor co-receptor CD8 -def: "A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction." [] +def: "A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction." [] is_a: PR:000000001 ! protein [Term] @@ -23683,6 +27116,53 @@ name: ribonuclease CL3 (chicken) def: "A protein with ribonuclease activity that is purified from chicken liver." [] is_a: PR:000000001 ! protein +[Term] +id: PR:000027247 +name: cytosolic creatine kinase complex, MB-type +def: "A cytosolic creatine kinase complex that is a heterodimer of a B-type subunit and an M-type subunit." [] +is_a: GO:0032991 ! protein-containing complex + +[Term] +id: PR:000029971 +name: creatine kinase +def: "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)." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000029983 +name: protein-glutamine gamma-glutamyltransferase +is_a: PR:000000001 ! protein + +[Term] +id: PR:000050219 +name: alanine aminotransferase +def: "A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000050331 +name: lactate dehydrogenase complex +def: "A protein-containing complex that is composed of four subunits of L-lactate dehydrogenase, cytoplasmic." [] +is_a: GO:0032991 ! protein-containing complex + +[Term] +id: PR:000050343 +name: alkaline phosphatase (human) +def: "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)." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000050353 +name: aspartate aminotransferase (human) +def: "A protein that is a translation product of any of the following genes in human: GOT1/GOT2." [] +is_a: PR:000000001 ! protein + +[Term] +id: PR:000050469 +name: hemoglobin A1c +def: "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." [] +is_a: GO:0032991 ! protein-containing complex + [Term] id: REO:0000171 name: obsolete molecular label role @@ -24056,11 +27536,6 @@ name: vein def: "Any of the tubular branching vessels that carry blood from the capillaries toward the heart." [] is_a: UBERON:0000465 ! material anatomical entity -[Term] -id: UBERON:0001707 -name: nasal cavity -def: "An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present." [] - [Term] id: UBERON:0001723 name: tongue @@ -24085,6 +27560,12 @@ name: vitreous humor def: "A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina" [] is_a: UBERON:0000463 ! organism substance +[Term] +id: UBERON:0001826 +name: nasal cavity mucosa +def: "The mucous membrane that lines the nasal cavity[MP]." [] +is_a: UBERON:0000465 ! material anatomical entity + [Term] id: UBERON:0001830 name: minor salivary gland diff --git a/views/obi_core.owl b/views/obi_core.owl index 91f29d0e..83c7cc12 100644 --- a/views/obi_core.owl +++ b/views/obi_core.owl @@ -12,7 +12,7 @@ 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 @@ -79,7 +79,7 @@ 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. - 2020-12-16 + 2021-04-06 @@ -119,13 +119,21 @@ + 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 @@ -161,7 +169,9 @@ 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 @@ -188,6 +198,7 @@ We also have the outstanding issue of how to aim different definitions to differ definition definition + textual definition @@ -1674,11 +1685,18 @@ every c that is a concretization of g specifically denotes r 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