diff --git a/Makefile b/Makefile index 6beb3cc3..c63271f3 100644 --- a/Makefile +++ b/Makefile @@ -207,6 +207,7 @@ views/obi_core.owl: obi.owl src/ontology/views/core.txt | build/robot.jar --term obo:OBI_0600036 \ --term obo:OBI_0600037 \ --term obo:OBI_0000838 \ + --term obo:OBI_0003071 \ --term APOLLO_SV:00000796 \ --select "self descendants" \ --preserve-structure false \ diff --git a/obi.owl b/obi.owl index e19c5346..a0c488d4 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 @@ -60,8 +60,8 @@ Mervi Heiskanen Monnie McGee Norman Morrison - Philip Lord Philippe Rocca-Serra + Phillip Lord Pierre Grenon Richard Bruskiewich Richard Scheuermann @@ -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. - 2021-04-06 + 2021-08-18 @@ -692,7 +692,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime + https://oborel.github.io/obo-relations/temporal-semantics/ @@ -4225,6 +4225,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ material MaterialEntity + material entity a flame a forest fire a human being @@ -4241,6 +4242,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) @@ -12193,6 +12195,18 @@ No imports + + + + + antibacterial + A material entity bearing an antibacterial disposition. + + antibacterial + + + + @@ -12285,6 +12299,9 @@ No imports Human gammaherpesvirus 4 Epstein Barr virus Epstein-Barr virus + Epstein-Barr virus EBV + Human herpesvirus 4 + Human herpesvirus type 4 Human gammaherpesvirus 4 @@ -12294,8 +12311,13 @@ No imports - + Hepatitis B virus + Human hepatitis B virus + hepatitis B virus (HBV) + hepatitis B virus HBV + hepatitis B virus, HBV + human hepatitis B virus HBV Hepatitis B virus @@ -12305,8 +12327,14 @@ No imports - + Hepacivirus C + Hepatitis C virus + hepatitis C virus HCV + human hepatitis C virus + human hepatitis C virus HCV + human hepatitis virus C HCV + post-transfusion hepatitis non A non B virus Hepacivirus C @@ -12316,8 +12344,9 @@ No imports - + Lentivirus + Lentivirinae Lentivirus @@ -12329,6 +12358,14 @@ No imports Human immunodeficiency virus 1 + human immunodeficiency virus 1 HIV-1 + human immunodeficiency virus HIV-1 + human immunodeficiency virus type 1 HIV 1 + human immunodeficiency virus type 1 HIV1 + human immunodeficiency virus type 1, HIV-1 + human immunodeficiency virus type I HIV-1 + human immunodeficiency virus type-1 HIV-1 + human immunodeficiency virus-1 HIV-1 Human immunodeficiency virus 1 @@ -12340,6 +12377,11 @@ No imports Human immunodeficiency virus 2 + HIV type 2 + Human immunodeficiency virus type 2 + Human immunodeficiency virus-2 + human immunodeficiency virus type 2 HIV-2 + human immunodeficiency virus type 2, HIV-2 Human immunodeficiency virus 2 @@ -12383,7 +12425,7 @@ No imports - + Pancrustacea Pancrustacea @@ -12414,6 +12456,30 @@ No imports + + + + + Riboviria + RNA viruses + RNA viruses and viroids + + Riboviria + + + + + + + + + Revtraviricetes + + Revtraviricetes + + + + @@ -12593,6 +12659,17 @@ No imports + + + + + Plasmodium + + Plasmodium + + + + @@ -12605,6 +12682,18 @@ No imports + + + + + Arthropoda + arthropods + + Arthropoda + + + + @@ -13204,7 +13293,7 @@ objectives is a planned process. chromatography device - A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a ""mobile phase"" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. + A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. Frank Gibson chromatography instrument http://en.wikipedia.org/wiki/Chromatography @@ -14037,7 +14126,8 @@ editor = PRS biological vector role - 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.|Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 + 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. + Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. GROUP: Role Branch @@ -15178,10 +15268,12 @@ An individual or juridicial or other body authorized under applicable law to con obsolete_blinded medication role - 115 patients received ipilimumab and blinded medication|Inert pill shaped like aspirin tablet + 115 patients received ipilimumab and blinded medication + Inert pill shaped like aspirin tablet Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance - Jennifer Fostel|Person:Helen Parkinson + Jennifer Fostel + Person:Helen Parkinson obsolete_blinded medication role true @@ -15581,7 +15673,8 @@ for now. Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. - PERSON: Jennifer Fostel|PERSON: Philippe Rocca-Serra + PERSON: Jennifer Fostel + PERSON: Philippe Rocca-Serra recruited population GROUP: OBI Biomaterial Branch @@ -15898,8 +15991,7 @@ for now. obsolete_enrollment - Enrollment of patients in a study. -Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 + Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules Bjoern Peters @@ -18065,8 +18157,7 @@ that has_part some material entity is a material entity. If we add as equivalent obsolete_identification - DNA cleavage assay for the identification of topoisomerase I inhibitors. -Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 + DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval Philippe Rocca-Serra @@ -18130,9 +18221,10 @@ Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 obsolete_defined_output example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. - This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. -Its children should be defined classes constructed as output of a process. - PERSON: Alan Ruttenberg|PERSON: James Malone|PERSON: Melanie Courtot + This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. + PERSON: Alan Ruttenberg + PERSON: James Malone + PERSON: Melanie Courtot obsolete_defined_output true @@ -19310,7 +19402,7 @@ Its children should be defined classes constructed as output of a process. - + @@ -19321,7 +19413,7 @@ Its children should be defined classes constructed as output of a process. - + @@ -22084,8 +22176,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. IEDB - ICS ICCS + ICS IEDB @@ -26140,7 +26232,7 @@ placeholder - western blot analysis + western blot assay Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest. An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. @@ -26148,7 +26240,7 @@ placeholder Philippe Rocca-Serra IEDB Philippe Rocca-Serra - western blot analysis + western blot assay @@ -31726,8 +31818,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S obsolete_specimen fixation function - A specimen -fixation function is a function that holds or fastens an entity in a fixed position. + A specimen fixation function is a function that holds or fastens an entity in a fixed position. EAGLE-I obsolete_specimen fixation function @@ -31938,7 +32029,7 @@ fixation function is a function that holds or fastens an entity in a fixed posit bioreactor - A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT + A device or system that supports a biologically active environment. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Bioreactor bioreactor @@ -34218,12 +34309,13 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - induced mutation + induced mutagenesis - a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. + A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation. + Label and definition were clarified as per https://github.com/obi-ontology/obi/issues/1366 PERSON: Chris Stoeckert, Jie Zheng MO_564 induced_mutation - induced mutation + induced mutagenesis @@ -43251,20 +43343,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - @@ -48635,6 +48713,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 + + + + + + @@ -48658,14 +48742,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 - far-Western blot assay + far-western blot assay Studying protein-protein interactions via blot overlay or Far Western blot. PMID:15064457 An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. Marcus Chibucos Philippe Rocca-Serra PMID:18079728 - far-Western blot assay + far-western blot assay @@ -59475,7 +59559,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Genome Analyzer IIx - Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. ""Lane-by-lane sequencing using Illumina's Genome Analyzer II."" BioTechniques 54.5 (2013): 265-269. PMID: 23662897 + Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59520,7 +59604,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Illumina HiSeq 2500 - Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 + Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59558,7 +59642,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Methylation 450K BeadChip - Naumov, Vladimir A., et al. ""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."" Epigenetics 8.9 (2013): 0-1. PMID: 23867710 + Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59574,7 +59658,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Methylation 27K BeadChip - Polidoro, Silvia, et al. ""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 + Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59590,7 +59674,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. 1M-Duo Infinium HD BeadChip - Edwards, Todd L., et al. ""Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease."" Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 + Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59612,7 +59696,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. SOLiD 3 Plus System - Vissers, Lisenka ELM, et al. ""A de novo paradigm for mental retardation."" Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 + Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59656,7 +59740,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Mouse 3x720K Whole Genome CGH Tiling Array - Wartman, Lukas D., et al. ""Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression."" The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 + Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59700,7 +59784,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Human 2.1M Whole-Genome CGH Tiling Array v2.0 - Filges, Isabel, et al. ""Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome."" Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 + Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59722,7 +59806,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. PacBio RS II - Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 + Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -59744,10 +59828,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. nCounter Human miRNA Expression array - Kolbert, Christopher P., et al. ""Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues."" PloS one 8.1 (2013): e52517. PMID:23382819 + Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed ""V2"" per https://github.com/obi-ontology/obi/issues/831 on 20180511. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed "V2" per https://github.com/obi-ontology/obi/issues/831 on 20180511. https://www.nanostring.com/products/mirna-assays/mirna-panels nCounter Human miRNA Expression array @@ -62414,13 +62498,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - + @@ -62434,7 +62512,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex - A B cell epitope assay that measures the on rate using a bio-layer interferometry assay. + A bio-layer interferometry assay that measures the on rate of a B cell epitope. IEDB IEDB on rate|bio-layer interferometry assay|M^-1s^-1 @@ -62446,13 +62524,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - + @@ -62466,7 +62538,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex - A B cell epitope assay that measures the off rate using a bio-layer interferometry assay. + A bio-layer interferometry assay that measures the off rate of a B cell epitope. IEDB IEDB off rate|bio-layer interferometry assay|1/s @@ -62478,16 +62550,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - + bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex - A B cell epitope qualitative binding to antibody assay that uses a bio-layer interferometry assay. + A bio-layer interferometry assay that detects a B cell epitope qualitative binding to antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|bio-layer interferometry assay @@ -62499,13 +62565,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - + @@ -62519,7 +62579,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a bio-layer interferometry assay. + A bio-layer interferometry assay that measures the dissociation constant [KD] of a B cell epitope binding. IEDB IEDB dissociation constant KD|bio-layer interferometry assay|nM @@ -64132,7 +64192,7 @@ https://www.doi.org/ - + @@ -69992,12 +70052,6 @@ https://www.doi.org/ - - - - - - file merge A data transformation in which data contained in 2 or more files are merged into a single file. @@ -70097,7 +70151,7 @@ https://www.doi.org/ nCounter Mouse miRNA Expression array - Kolbert, Christopher P., et al. ""Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues."" PloS one 8.1 (2013): e52517. PMID:23382819 + Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 @@ -71451,7 +71505,7 @@ https://www.doi.org/ Illumina NovaSeq 6000 - ""Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system."" + Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. Dan Berrios @@ -71502,7 +71556,7 @@ https://www.doi.org/ PacBio Sequel II The cDNAs were sequenced on the PacBio Sequel II platform. - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (""HiFi"") long reads, and which is manufactured by the Pacific Biosciences corporation. + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. Bonita Lam Dan Berrios Pacific BioSciences Sequel II @@ -71919,6 +71973,7 @@ https://www.doi.org/ + @@ -71961,7 +72016,7 @@ https://www.doi.org/ - + @@ -72173,6 +72228,7 @@ https://www.doi.org/ A biopsy involving a surgical incision into an organism to access the biopsy material. Damion Dooley + excisional biopsy open biopsy https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 surgical biopsy @@ -74368,7 +74424,7 @@ https://www.doi.org/ - + @@ -74385,10 +74441,10 @@ https://www.doi.org/ - + pathogen detection assay - An assay that aims to detect pathogens. + An organism identification assay that aims to detect pathogens. VEuPathDB pathogen detection method IRO:0000137 @@ -75549,7 +75605,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre tracheal aspirate specimen A specimen that is collected with a suctioning tube from the trachea. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 tracheal wash specimen PMID:25338241 tracheal aspirate specimen @@ -75589,7 +75645,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre mid-turbinate nasal swab specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 mid-turbinate nasal swab specimen @@ -75628,9 +75684,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre nasal aspirate specimen A specimen that is collected with a suctioning tube from the nasal cavity. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal wash specimen|nasopharyngeal aspirate - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal aspirate specimen @@ -75668,9 +75724,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre lower respiratory tract aspirate specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract wash specimen - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract aspirate specimen @@ -75708,8 +75764,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre upper respiratory specimen A specimen that is derived from the upper respiratory tract - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 upper respiratory specimen @@ -75747,8 +75803,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre lower respiratory tract specimen A specimen that is derived from the lower respiratory tract. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract specimen @@ -75786,8 +75842,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre anterior nasal swab specimen A specimen that is derived from the anterior nasal wall - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 anterior nasal swab specimen @@ -76216,7 +76272,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - protective apron @@ -76732,7 +76787,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A device designed to catch arthropods. John Judkins - trap catch MIRO:30000011 https://github.com/obi-ontology/obi/issues/1217 arthropod trap @@ -76777,7 +76831,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -76799,7 +76852,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -76821,7 +76873,6 @@ 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 IRO:0000028 VSMO:0001906 https://github.com/obi-ontology/obi/issues/1217 @@ -76836,9 +76887,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre Centers for Disease Control and Prevention light trap - A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. + 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 + CDC light trap IRO:0000163 https://github.com/obi-ontology/obi/issues/1217 Centers for Disease Control and Prevention light trap @@ -76870,7 +76922,7 @@ 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 + EVS trap IRO:0000029 VSMO:0001295 https://github.com/obi-ontology/obi/issues/1217 @@ -76887,7 +76939,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -76903,7 +76954,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -76919,7 +76969,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A light trap designed to be placed inside a building. John Judkins - indoor light trap catch + indoor light trap MIRO:30000009 https://github.com/obi-ontology/obi/issues/1217 light trap for indoor use @@ -76935,7 +76985,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A light trap designed to be placed outside a building. John Judkins - outdoor light trap catch + outdoor light trap MIRO:30000010 https://github.com/obi-ontology/obi/issues/1217 light trap for outdoor use @@ -76951,7 +77001,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -76982,7 +77031,7 @@ 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 light attractant. John Judkins - new jersey trap catch + New Jersey trap IRO:0000031 https://github.com/obi-ontology/obi/issues/1217 New Jersey light trap @@ -77015,7 +77064,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + outlet window trap MIRO:30000020 https://github.com/obi-ontology/obi/issues/1217 outlet window trap @@ -77149,266 +77198,978 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + + - - - - - - - - - - - - - + + + + - endotracheal tube specimen + + + + + + + + + + + + + + + + + fluorescence imaging-based apoptosis assay - 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 + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/1 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based apoptosis assay - + - - + + + - - - - - - - - - - - - - + + + + - endotracheal aspirate specimen + + + + + + + + + + + + + + + + + fluorescence imaging-based cell proliferation assay - 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 + A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + fluroescence imaging-based cell count assay + url:http://lincsportal.ccs.miami.edu/beta/assays/31 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell proliferation assay - + - - - 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. + + + + + + + + + + + + + + + + + + + + + + + + + + fluroescence imaging-based cell cycle state assay - 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 + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/10 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluroescence imaging-based cell cycle state assay - + - - - 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. + + + + + + + + + + + + + + + + + + + + + + + + + + fluorescence imaging-based cell viability assay - 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 + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/27 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell viability assay - + - - - 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. + + + + + + + + + + + + + + + + + + + + + + + + + + fluorescence imaging-based drug synergy assay - The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). - Emma Griffiths - input gene start - query gene start site - Emma Griffiths - input gene sequence start site + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/7 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based drug synergy assay - + - - - 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. + + + + + + + + + + + + + + + + + + + + + + + + + + fluorescence imaging-based cell morphology assay - 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 + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell morphology assay - + - - - 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. + + + + + + + + + + + + + + + + + + + + + + + + + + fluorescence imaging multiplex cytological profiling - 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 + A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/8 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging multiplex cytological profiling - + - - - 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. + + + protein state assay - 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 + A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + protein state assay - + - - - 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. + + + + + + + + + + + + + + + + + + + + + + + + + + fluorescence imaging-based protein phosphorylation state assay - 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 + A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/15 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based protein phosphorylation state assay - + - - - 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. + + + + + + + + + mass spectrometry-based protein state assay - 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 + A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + mass spectrometry-based protein state assay - + - - - altitude measurement datum + + + targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay - 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 + A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + P100 phosphoprotein quantification assay + PMID:26912667 + PMID:29655704 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay - + - - - 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. + + + reverse phase protein array profiling assay - 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 + A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + RPLA assay + RPPA assay + reverse phase lysate array profiling assay + PMID: 17041095 + PMID:31820393 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + reverse phase protein array profiling assay - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - magnetic resonance imaging assay + SWATH-MS protein profiling 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. + A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. + Michelle Giglio Rebecca Jackson - MRI - url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging - https://github.com/obi-ontology/obi/issues/1290 + Suvarna Nadendla + sequential window acquisition of all theoretical mass spectra protein profiling assay + PMID:30104418 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + SWATH-MS protein profiling assay + + + + + + + + + tandem mass tag mass spectrometry + + A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:12713048 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + tandem mass tag mass spectrometry + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + fluorescence imaging-based reporter gene assay + + A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based reporter gene assay + + + + + + + + + + + + + + + + + + + + + global chromatin profiling by mass spectrometry assay + + A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + GCP + global chromatin epigenetic profiling + global chromatin profiling + PMID:25448295 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + global chromatin profiling by mass spectrometry assay + + + + + + + + + kinase inhibitor assay + + A type of assay that identifies compounds that inhibit the activity of kinases. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + kinase inhibitor assay + + + + + + + + + KINOMEscan assay + + A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.discoverx.com/technologies-platforms/competitive-binding-technology/kinomescan-technology-platform + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + KINOMEscan assay + + + + + + + + + KiNativ assay + + A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.kinativ.com/technology.html + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + KiNativ assay + + + + + + + + + landmark transcript profiling assay + + A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + L1000 mRNA profiling assay + PMID:29195078 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + landmark transcript profiling assay + + + + + + + + + microenvironment microarray assay + + A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + MEMA assay + PMID:29199020 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + microenvironment microarray assay + + + + + + + + + microwestern meso-scale quantitative western blot assay + + A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:28092050 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + microwestern meso-scale quantitative western blot assay + + + + + + + + + + + + + + + positive/negative ion switching metabolite profiling assay + + A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + positive/negative ion switching metabolomic assay + PMID:22498707 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + positive/negative ion switching metabolite profiling assay + + + + + + + + + cyclic immunoflouroescence assay + + A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:27925668 + PMID:29993362 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + cyclic immunoflouroescence assay + + + + + + + + + multiplex bead-based protein state immunoassay + + A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.bio-rad.com/en-us/applications-technologies/multiplex-immunoassays?ID=LUSM0E8UU + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + multiplex bead-based protein state immunoassay + + + + + + + + + + + + + + + + + + + + + + + + endotracheal tube specimen + + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. + John Judkins ORCID:0000-0001-6595-0902 + https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 + endotracheal tube specimen + + + + + + + + + + + + + + + + + + + + + + + + endotracheal aspirate specimen + + A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected 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 + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + magnetic resonance imaging assay + + An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. + Rebecca Jackson + MRI + url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging + https://github.com/obi-ontology/obi/issues/1290 magnetic resonance imaging assay @@ -77797,14 +78558,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - device for resting of adult arthropods for collection + device for collection of resting adult arthropods A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. John Judkins VSMO:0001355 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB - device for resting of adult arthropods for collection + device for collection of resting adult arthropods @@ -78493,6 +79254,1332 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + barcode target locus role + + An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. + Chris Stoeckert https://orcid.org/0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1325 + barcode target locus role + + + + + + + + + + + + + + + oligonucleotide primer set + + A processed material that consists of oligonucleotides that bear a primer role. + Chris Stoeckert https://orcid.org/0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1325 + oligonucleotide primer set + + + + + + + + + fluorogenic PCR assay + + A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. + John Judkins + TaqMan + MIRO:20000102 + https://github.com/obi-ontology/obi/issues/1320 + fluorogenic PCR assay + + + + + + + + + + + + + + + + genotyping by PCR assay + genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci. + + A genotyping assay that uses polymerase chain reaction. + Chris Stoeckert, ORCID:0000-0002-5714-991X + Jie Zheng, ORCID:0000-0002-2999-0103 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1348 + VEuPathDB + genotyping by PCR assay + + + + + + + + + cleavage under targets and release using nuclease assay + + A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CUT&RUN assay + url:https://elifesciences.org/articles/21856 + https://github.com/obi-ontology/obi/issues/1192 + bonitalam + cleavage under targets and release using nuclease assay + + + + + + + + + cleavage under targets and tagmentation + + A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CUT&Tag assay + url:https://www.nature.com/articles/s41467-019-09982-5 + https://github.com/obi-ontology/obi/issues/1192 + bonitalam + cleavage under targets and tagmentation + + + + + + + + + coma severity assay + Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. + + A physical examination of individual that has the objective to determine the severity of coma in a patient. + John Judkins + https://github.com/obi-ontology/obi/issues/1357 + John Judkins + coma severity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Plasmodium gametocyte detection assay + + An assay that detects Plasmodium gametocytes in a specimen. + Chris Stoeckert + Jie Zheng + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + Plasmodium gametocyte detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + malaria rapid diagnosis assay + + An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. + Chris Stoeckert + Jie Zheng + malaria rapid diagnosis test + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + malaria rapid diagnosis assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + parasite detection assay + + An assay that detects parasite in a specimen. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + feces microbiology assay + + An assay that detects microorganisms in a feces specimen. + John Judkins + stool test for microorganisms + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + feces microbiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood assay + + An assay that has a blood specimen as evaulant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + blood assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + falcivax rapid diagnostic test + + A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + falcivax rapid diagnostic test + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + optimal-IT rapid diagnostic test + + A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + optimal-IT rapid diagnostic test + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine assay + + An assay that has a urine specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + urine assay + + + + + + + + + + + + + + + parasite species identification by PCR assay + + An organism identification assay that identifies the species of parasites by PCR. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite species identification by PCR assay + + + + + + + + + + + + + + + + + + + + + + parasite detection by PCR assay + + An assay that detects parasite in a specimen using PCR. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite detection by PCR assay + + + + + + + + + free-standing window trap + Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658] + + An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die. + VEuPathDB + VSMO:0001649 + free-standing window trap + + + + + + + + + + + + + + + BG-lure scent dispenser + + A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin. + VEuPathDB + BG-lure + IRO:0001060 + BG-lure scent dispenser + + + + + + + + + hand-held sweep net + + A device that consists of a network of mesh and is designed to capture adult arthropods. + VEuPathDB + VSMO:0001522 + hand-held sweep net + + + + + + + + + Centers for Disease Control and Prevention gravid trap + The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658] + + A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan. + VEuPathDB + CDC gravid trap + VSMO:0001510 + Centers for Disease Control and Prevention gravid trap + + + + + + + + + egg specimen collection process + + An arthropod specimen collection process in which the arthropods are in the embryo stage. + VEuPath + collection of eggs + MIRO:30000049 + https://github.com/obi-ontology/obi/issues/1322 + egg specimen collection process + + + + + + + + + larval specimen collection process + + An arthropod specimen collection process in which the arthropods are in the larval stage. + VEuPath + collection of larvae + MIRO:30000022 + https://github.com/obi-ontology/obi/issues/1322 + larval specimen collection process + + + + + + + + + pupal specimen collection process + + An arthropod specimen collection process in which the arthropods are in the pupal stage. + VEuPath + collection of pupae + MIRO:30000050 + https://github.com/obi-ontology/obi/issues/1322 + pupal specimen collection process + + + + + + + + + + + + + + + + + + + + + + + + blood specimen in vacutainer + + A blood specimen that is located in a vacutainer. + John Judkins + Vacutainer sample + VEuPathDB + blood specimen in vacutainer + + + + + + + + + + + + + + + + + + + + + + + + blood specimen on filter paper + + A blood specimen that is located on a filter paper. + Chris Stoeckert + Jie Zheng + Filter paper sample + Penn Group + blood specimen on filter paper + + + + + + + + + proportion mapped reads + + A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads. + John Judkins + VEuPathDB + proportion mapped reads + + + + + + + + + + + + + + + + + + + + + + + + + antibiotic administration process + + Administering substance in vivo where an antibiotic substance is administered to a living organism. + Chris Stoeckert + Cristian Cocos + Jie Zheng + Penn Group + antibiotic administration process + + + + + + + + + insecticide resistance datum + + A data item that is about resistance to an insecticide. + John Judkins + VEuPathDB + insecticide resistance datum + + + + + + + + + organism identification datum + + A data item that is the specified output of an organism identification assay. + John Judkins + VEuPathDB + organism identification datum + + + + + + + + + easting coordinate measurement datum + + A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. + Easting and northing coordinates are commonly measured in meters from a horizontal datum. + John Judkins + https://en.wikipedia.org/wiki/Grid_reference_system + easting coordinate measurement datum + + + + + + + + + northing coordinate measurement datum + + A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. + Easting and northing coordinates are commonly measured in meters from a horizontal datum. + John Judkins + https://en.wikipedia.org/wiki/Grid_reference_system + northing coordinate measurement datum + + + + + + + + + clinical study center + + Organization that undertakes a clinical study at some point in time. + Chris Stoeckert + Cristian Cocos + Jie Zheng + Penn Group + clinical study center + + + + + + + + + sequencing protocol + + A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. + John Judkins + VEuPathDB + sequencing protocol + + + + + + + + + + + + + + + specimen collection protocol + + A protocol that specifies processes to fulfill a specimen collection objective. + John Judkins + VEuPathDB + specimen collection protocol + + + + + + + + + + + + + + + + + + + + + + + + + participant identifier + + A symbol that denotes a participant under investigation. + John Judkins + VEuPathDB + participant identifier + + + + + + + + + axillary temperature measurement datum + + A temperature measurement datum that is about an axilla. + John Judkins + VEuPathDB + axillary temperature measurement datum + + + + + + + + + organismal body temperature measurement datum + + A temperature measurement datum that is about an organism. + Chris Stoeckert + Jie Zheng + Penn Group + organismal body temperature measurement datum + + + + + + + + + + + + + + + common name of organism + + A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized. + John Judkins + https://en.wikipedia.org/wiki/Common_name + common name of organism + + + + + + + + + age since birth at time of enrollment + + An age since birth measurement datum at the time of subject enrollment. + Jie Zheng + Penn Group + age since birth at time of enrollment + + + + + + + + + age since birth at time of visit + + An age since birth measurement datum at the time of a clinical visit. + Chris Stoeckert + Grant Dorsey + Jie Zheng + Shon Cade + Penn Group + age since birth at time of visit + + + + + + + + + entomological data item + + A data item that is about a collection of insects. + John Judkins + entomological measurement datum + VEuPathDB + entomological data item + + + + + + + + + temperature measurement datum + + A scalar measurement datum that is the result of measuring temperature. + John Judkins + VEuPathDB + temperature measurement datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organismal body temperature measurement assay + + An assay that detects body temperature of an organism. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + organismal body temperature measurement assay + + + + + + + + + extraction date + + A time measurement datum that specifies when some material was extracted from an input material. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + FLU, VEuPathDB + https://github.com/obi-ontology/obi/issues/1286 + extraction date + + + + + + + + + extraction duration time + + A time measurement datum that is the result of measuring the duration of an extraction process. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + Meredith Keybl, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + extraction duration time + + + + + + + + + specimen collection time post disease onset + + A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + GROUP:FLU, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + specimen collection time post disease onset + + + + + + + + + specimen collection time post infection + + A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + VEuPathDB, EUPATH:0000613 + https://github.com/obi-ontology/obi/issues/1286 + specimen collection time post infection + + + + + + + + + laboratory postal address + + A postal address used as a directive to deliver something to a laboratory. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + laboratory address + GROUP:FLU, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + laboratory postal address + + + + + + + + + laboratory-based population + Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033) + + A population where the collection of individuals is located and maintained in a laboratory, research, or production facility. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1370 + laboratory-based population + + + + + + + + + + + + + + + Illumina MiniSeq + Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526 + + A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + PERSON: Bonita Lam + MiniSeq + url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html + Illumina MiniSeq + + + + @@ -78569,7 +80656,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + Bjoern Peters + Philippe Rocca-Serra + Tina Boussard MO obsolete_anatomical entity @@ -78843,7 +80932,8 @@ This issue is outside the scope of OBI. 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 + immortal cell line sample + permanent cell line PERSON:Matthew Brush @@ -78977,7 +81067,8 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from 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 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 @@ -79130,7 +81221,8 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ obsolete_polymer A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. - James Malone|Philippe Rocca-Serra + James Malone + Philippe Rocca-Serra TERM: CHEBI:33839 obsolete_polymer @@ -83202,8 +85294,8 @@ determinations of compounds. a collection is a bfo:aggregate object, that is a set of material object of the same kind PERSON: Susanna Sansone - ensemble - group + ensemble + group set PERSON: Philippe Rocca-Serra @@ -83374,6 +85466,7 @@ determinations of compounds. + @@ -83556,8 +85649,7 @@ determinations of compounds. obsolete_liver - PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. -AJR Am J Roentgenol. 1990 Jan;154(1):87-93. + 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 @@ -84272,8 +86364,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 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!) + 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 @@ -85014,11 +87105,11 @@ Manual editing of automatically recorded data in an anesthesia information manag FACS Calibur - ""FACS Calibur at TFL, BCCRC, Vancouver"" + 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"" + http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11 FACS Calibur @@ -85999,7 +88090,7 @@ Manual editing of automatically recorded data in an anesthesia information manag 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"" + http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10 SomaScope @@ -86613,7 +88704,7 @@ Manual editing of automatically recorded data in an anesthesia information manag 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. + 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 @@ -86826,7 +88917,7 @@ Manual editing of automatically recorded data in an anesthesia information manag DNA microarray - Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). ""Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis"". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 + 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 @@ -92740,6 +94831,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it + 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. @@ -93290,8 +95382,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 uterine cervix specimen @@ -93323,8 +95417,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 urethra specimen @@ -93356,8 +95452,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 cervical mucus specimen @@ -93389,8 +95487,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 throat specimen @@ -93422,8 +95522,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 eye specimen @@ -93455,8 +95557,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 respiratory system specimen @@ -93488,8 +95592,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 upper respiratory tract specimen @@ -93521,8 +95627,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 nasopharynx specimen @@ -93554,8 +95662,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 semen specimen @@ -93587,8 +95697,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 bodily fluid specimen @@ -93620,8 +95732,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 chorionic villus specimen @@ -93653,8 +95767,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 meconium specimen @@ -93686,8 +95802,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 umbilical cord blood specimen @@ -93719,8 +95837,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 arterial blood specimen @@ -93752,8 +95872,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 venous blood specimen @@ -93785,8 +95907,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 capillary blood specimen @@ -93820,8 +95944,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 erythrocyte specimen @@ -93855,8 +95981,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 reticulocyte specimen @@ -93890,8 +96018,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 leukocyte specimen @@ -100555,7 +102685,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -101684,6 +103814,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -101757,6 +103888,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -101830,6 +103962,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -101903,6 +104036,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -102182,6 +104316,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -102255,6 +104390,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -106457,6 +108593,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -110277,6 +112414,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -110569,6 +112707,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -113022,6 +115161,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -117598,6 +119738,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + @@ -117840,31 +119981,297 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + + + + + + + + + + venous blood nucleated RBC count assay + + A cytometry assay that measures the count of nucleated RBCs in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood nucleated RBC count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + venous blood WBC count assay + + A cytometry assay that measures the count of WBCs in venous blood + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + venous blood WBC count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + automated count venous blood reticulocyte count assay + + A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + automated count venous blood reticulocyte count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + total venous blood homocysteine assay + + An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + total venous blood homocysteine assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + + + + + - venous blood nucleated RBC count assay + venous blood Ceruloplasmin assay - A cytometry assay that measures the count of nucleated RBCs in venous blood + 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 nucleated RBC count assay + venous blood Ceruloplasmin assay - + - - + + @@ -117876,7 +120283,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -117887,7 +120294,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -117900,31 +120307,44 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - venous blood WBC count assay + GEM4 arterial blood bicarbonate assay - A cytometry assay that measures the count of WBCs in venous blood + 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 - venous blood WBC count assay + GEM4 arterial blood bicarbonate assay - + - - + + @@ -117936,7 +120356,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -117947,7 +120367,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -117965,26 +120385,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - automated count venous blood reticulocyte count assay + GEM4 arterial blood lactic acid assay - A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order + 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 - automated count venous blood reticulocyte count assay + GEM4 arterial blood lactic acid assay - + - - + + @@ -117996,7 +120416,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118007,7 +120427,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118030,7 +120450,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118038,26 +120458,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - total venous blood homocysteine assay + GEM4 arterial blood hemoglobin assay - An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order + 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 - total venous blood homocysteine assay + GEM4 arterial blood hemoglobin assay - + - - + + @@ -118069,7 +120489,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118080,7 +120500,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118103,7 +120523,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118111,26 +120531,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - venous blood Ceruloplasmin assay + GEM4 arterial blood sodium assay - An analyte assay that measures the abundance of Ceruloplasmin in venous blood + 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 - venous blood Ceruloplasmin assay + GEM4 arterial blood sodium assay - + - - + + @@ -118176,7 +120596,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118184,26 +120604,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - GEM4 arterial blood bicarbonate assay + GEM4 arterial blood potassium assay - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order + 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 bicarbonate assay + GEM4 arterial blood potassium assay - + - - + + @@ -118244,26 +120664,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - GEM4 arterial blood lactic acid assay + GEM4 arterial blood temperature assay - An assay that measures lactic acid in arterial blood as part of a GEM4 order + 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 lactic acid assay + GEM4 arterial blood temperature assay - + - - + + @@ -118309,7 +120729,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118317,26 +120737,99 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - GEM4 arterial blood hemoglobin assay + GEM4 arterial blood glucose assay - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order + 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 hemoglobin assay + GEM4 arterial blood glucose assay - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GEM4 arterial blood oxygen assay + + An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + GEM4 arterial blood oxygen assay + + + + + + + + @@ -118372,44 +120865,32 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - GEM4 arterial blood sodium assay + GEM4 arterial blood hematocrit assay - An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order + 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 sodium assay + GEM4 arterial blood hematocrit assay - + - - + + + @@ -118455,7 +120936,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118463,26 +120944,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - GEM4 arterial blood potassium assay + GEM4 arterial blood ionized calcium assay - An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order + 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 potassium assay + GEM4 arterial blood ionized calcium assay - + - - + + @@ -118518,31 +120999,44 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - GEM4 arterial blood temperature assay + GEM4 arterial blood carbon dioxide assay - An assay that measures temperature in arterial blood as part of a GEM4 order + 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 temperature assay + GEM4 arterial blood carbon dioxide assay - + - - + + @@ -118554,7 +121048,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118565,7 +121059,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118578,44 +121072,31 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - GEM4 arterial blood glucose assay + liver fibrosis (NAFLD) venous blood platelet count assay - An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order + 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 - GEM4 arterial blood glucose assay + liver fibrosis (NAFLD) venous blood platelet count assay - + - - + + @@ -118627,7 +121108,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118638,7 +121119,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118661,7 +121142,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118669,26 +121150,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - GEM4 arterial blood oxygen assay + venous blood beta hydroxybutric acid assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order + 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 - GEM4 arterial blood oxygen assay + venous blood beta hydroxybutric acid assay - + - - + + @@ -118700,7 +121181,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118711,7 +121192,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118729,27 +121210,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - GEM4 arterial blood hematocrit assay + CBC with manual differential venous blood plasma cell count assay - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order + 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 - GEM4 arterial blood hematocrit assay + CBC with manual differential venous blood plasma cell count assay - + - - - + + @@ -118761,7 +121241,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118772,7 +121252,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118795,7 +121275,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118803,26 +121283,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - GEM4 arterial blood ionized calcium assay + venous blood erythropoietin assay - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order + 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 - GEM4 arterial blood ionized calcium assay + venous blood erythropoietin assay - + - - + + @@ -118868,46 +121348,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - + @@ -118915,47 +121356,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - + - - - - - - - - - - - - liver fibrosis (NAFLD) venous blood platelet count assay + blood gas arterial blood oxygen assay - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order + 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 - liver fibrosis (NAFLD) venous blood platelet count assay + blood gas arterial blood oxygen assay - + - - + + @@ -118967,7 +121387,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -118978,7 +121398,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119001,7 +121421,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119009,26 +121429,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - venous blood beta hydroxybutric acid assay + blood gas arterial blood bicarbonate assay - An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood + 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 - venous blood beta hydroxybutric acid assay + blood gas arterial blood bicarbonate assay - + - - + + @@ -119040,7 +121460,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119051,7 +121471,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119064,31 +121484,44 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - CBC with manual differential venous blood plasma cell count assay + blood gas arterial blood carbon dioxide assay - A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order + 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 - CBC with manual differential venous blood plasma cell count assay + blood gas arterial blood carbon dioxide assay - + - - + + @@ -119134,7 +121567,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119142,26 +121575,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - venous blood erythropoietin assay + free/total venous blood PSA assay - An analyte assay that measures the abundance of erythropoietin in venous blood + 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 - venous blood erythropoietin assay + free/total venous blood PSA assay - + - - + + @@ -119173,7 +121606,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119184,7 +121617,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119197,44 +121630,31 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - blood gas arterial blood oxygen assay + cerebrospinal fluid lymphocyte count assay - An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order + 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 - blood gas arterial blood oxygen assay + cerebrospinal fluid lymphocyte count assay - + - - + + @@ -119246,7 +121666,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119257,7 +121677,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119270,44 +121690,31 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - blood gas arterial blood bicarbonate assay + cerebrospinal fluid segmented neutrophil count assay - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order + 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 - blood gas arterial blood bicarbonate assay + cerebrospinal fluid segmented neutrophil count assay - + - - + + @@ -119319,7 +121726,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119330,7 +121737,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119343,44 +121750,31 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - blood gas arterial blood carbon dioxide assay + cerebrospinal fluid mesothelial cell count assay - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order + 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 - blood gas arterial blood carbon dioxide assay + cerebrospinal fluid mesothelial cell count assay - + - - + + @@ -119392,7 +121786,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119403,7 +121797,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119416,44 +121810,31 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - free/total venous blood PSA assay + cerebrospinal fluid macrophage count assay - An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order + 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 - free/total venous blood PSA assay + cerebrospinal fluid macrophage count assay - + - - + + @@ -119494,26 +121875,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - cerebrospinal fluid lymphocyte count assay + cerebrospinal fluid basophil count assay - A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid + 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 lymphocyte count assay + cerebrospinal fluid basophil count assay - + - - + + @@ -119554,26 +121935,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - cerebrospinal fluid segmented neutrophil count assay + cerebrospinal fluid monocyte count assay - A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid + 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 segmented neutrophil count assay + cerebrospinal fluid monocyte count assay - + - - + + @@ -119614,26 +121995,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - cerebrospinal fluid mesothelial cell count assay + cerebrospinal fluid eosinophil count assay - A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid + 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 mesothelial cell count assay + cerebrospinal fluid eosinophil count assay - + - - + + @@ -119645,7 +122026,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119656,7 +122037,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119668,32 +122049,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - cerebrospinal fluid macrophage count assay - - A cytometry assay that measures the count of macrophages in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid macrophage count assay - - - - - - - - @@ -119702,10 +122057,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - - + + @@ -119713,47 +122068,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - + - - - - - - - - - - - - cerebrospinal fluid basophil count assay + venous blood beta-2-microglobulin assay - A cytometry assay that measures the count of basophils in cerebrospinal fluid + 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 - cerebrospinal fluid basophil count assay + venous blood beta-2-microglobulin assay - + - - + + @@ -119765,7 +122099,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119776,7 +122110,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119788,32 +122122,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - cerebrospinal fluid monocyte count assay - - A cytometry assay that measures the count of monocytes in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid monocyte count assay - - - - - - - - @@ -119822,10 +122130,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - - + + @@ -119833,47 +122141,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - + - - - - - - - - - - - - cerebrospinal fluid eosinophil count assay + lipid panel reflex direct venous blood low density lipoprotein assay - A cytometry assay that measures the count of eosinophils in cerebrospinal fluid + 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 - cerebrospinal fluid eosinophil count assay + lipid panel reflex direct venous blood low density lipoprotein assay - + - - + + @@ -119919,7 +122206,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -119927,26 +122214,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - venous blood beta-2-microglobulin assay + lipid panel reflex direct venous blood triglyceride assay - An analyte assay that measures the abundance of beta-2-microglobulin in venous blood + 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 - venous blood beta-2-microglobulin assay + lipid panel reflex direct venous blood triglyceride assay - + - - + + @@ -119992,7 +122279,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -120000,26 +122287,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - lipid panel reflex direct venous blood low density lipoprotein assay + lipid panel reflex direct venous blood cholesterol assay - An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order + 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 low density lipoprotein assay + lipid panel reflex direct venous blood cholesterol assay - + - - + + @@ -120065,7 +122352,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -120073,60 +122360,26 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - lipid panel reflex direct venous blood triglyceride assay + lipid panel reflex direct venous blood high density lipoprotein assay - An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order + 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 triglyceride assay + lipid panel reflex direct venous blood high density lipoprotein assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -120135,10 +122388,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - + @@ -120146,26 +122399,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - lipid panel reflex direct venous blood cholesterol assay - - An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel reflex direct venous blood cholesterol assay - - - - - - - - @@ -120177,7 +122415,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -120188,7 +122426,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -120201,36 +122439,20 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - - - - - - - + + + + - lipid panel reflex direct venous blood high density lipoprotein assay + pooled clone sequencing assay + Although a similar pooled clone sequencing method has recently been described by others for metagenome-derived medium-insert plasmids and large-insert fosmids, to our knowledge, we are the first to report the pooled strategy for sequencing of large-insert metagenomic clones while also critically evaluating the performance of this pooled strategy by comparing the results to barcoded reference sequences of the same clones. - 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 + A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. + Dan Berrios, ORCID: 0000-0003-4312-9552 + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049660/ + https://github.com/obi-ontology/obi/issues/1106 + Bonita Lam + pooled clone sequencing assay @@ -120405,6 +122627,30 @@ realizes some 'host of immune response role' + + + + + parasite organism + An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. + + parasite organism + + + + + + + + + Plasmodium gametocyte + A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes + + Plasmodium gametocyte + + + + @@ -124356,12 +126602,6 @@ realizes some 'host of immune response role' - - - - - - right handed right handed @@ -124373,12 +126613,6 @@ realizes some 'host of immune response role' - - - - - - ambidexterous ambidexterous @@ -124390,12 +126624,6 @@ realizes some 'host of immune response role' - - - - - - left handed left handed diff --git a/views/NIAID-GSC-BRC.owl b/views/NIAID-GSC-BRC.owl index 2d8b5505..d66b86a3 100644 --- a/views/NIAID-GSC-BRC.owl +++ b/views/NIAID-GSC-BRC.owl @@ -7,12 +7,11 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg @@ -58,8 +57,8 @@ Mervi Heiskanen Monnie McGee Norman Morrison - Philip Lord Philippe Rocca-Serra + Phillip Lord Pierre Grenon Richard Bruskiewich Richard Scheuermann @@ -78,7 +77,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2021-04-06 + 2021-08-18 @@ -338,7 +337,7 @@ We also have the outstanding issue of how to aim different definitions to differ An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime + https://oborel.github.io/obo-relations/temporal-semantics/ @@ -349,12 +348,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - + + + + + @@ -3642,6 +3648,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -3684,6 +3696,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -3756,6 +3774,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + @@ -4253,7 +4277,7 @@ objectives is a planned process. chromatography device - A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a ""mobile phase"" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. + A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. Frank Gibson chromatography instrument http://en.wikipedia.org/wiki/Chromatography @@ -5080,7 +5104,8 @@ editor = PRS - 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.|Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 + 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. + Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. GROUP: Role Branch @@ -6205,10 +6230,12 @@ An individual or juridicial or other body authorized under applicable law to con - 115 patients received ipilimumab and blinded medication|Inert pill shaped like aspirin tablet + 115 patients received ipilimumab and blinded medication + Inert pill shaped like aspirin tablet Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance - Jennifer Fostel|Person:Helen Parkinson + Jennifer Fostel + Person:Helen Parkinson obsolete_blinded medication role true @@ -6606,7 +6633,8 @@ for now. Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. - PERSON: Jennifer Fostel|PERSON: Philippe Rocca-Serra + PERSON: Jennifer Fostel + PERSON: Philippe Rocca-Serra recruited population GROUP: OBI Biomaterial Branch @@ -6919,8 +6947,7 @@ for now. - Enrollment of patients in a study. -Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 + Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules Bjoern Peters @@ -9061,8 +9088,7 @@ that has_part some material entity is a material entity. If we add as equivalent - DNA cleavage assay for the identification of topoisomerase I inhibitors. -Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 + DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval Philippe Rocca-Serra @@ -9124,9 +9150,10 @@ Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. - This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. -Its children should be defined classes constructed as output of a process. - PERSON: Alan Ruttenberg|PERSON: James Malone|PERSON: Melanie Courtot + This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. + PERSON: Alan Ruttenberg + PERSON: James Malone + PERSON: Melanie Courtot obsolete_defined_output true @@ -10298,7 +10325,7 @@ Its children should be defined classes constructed as output of a process. - + @@ -10309,7 +10336,7 @@ Its children should be defined classes constructed as output of a process. - + @@ -13056,8 +13083,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. IEDB - ICS ICCS + ICS IEDB @@ -17063,7 +17090,7 @@ placeholder Philippe Rocca-Serra IEDB Philippe Rocca-Serra - western blot analysis + western blot assay @@ -22530,8 +22557,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - A specimen -fixation function is a function that holds or fastens an entity in a fixed position. + A specimen fixation function is a function that holds or fastens an entity in a fixed position. EAGLE-I obsolete_specimen fixation function @@ -22740,7 +22766,7 @@ fixation function is a function that holds or fastens an entity in a fixed posit bioreactor - A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT + A device or system that supports a biologically active environment. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Bioreactor bioreactor @@ -25011,12 +25037,13 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - induced mutation + induced mutagenesis - a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation. + A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation. + Label and definition were clarified as per https://github.com/obi-ontology/obi/issues/1366 PERSON: Chris Stoeckert, Jie Zheng MO_564 induced_mutation - induced mutation + induced mutagenesis @@ -33481,20 +33508,6 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - - - - - - - - - - - - - - @@ -38554,6 +38567,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 + + + + + + @@ -38583,7 +38602,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891 Marcus Chibucos Philippe Rocca-Serra PMID:18079728 - far-Western blot assay + far-western blot assay @@ -48718,7 +48737,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. ""Lane-by-lane sequencing using Illumina's Genome Analyzer II."" BioTechniques 54.5 (2013): 265-269. PMID: 23662897 + Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48761,7 +48780,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 + Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48797,7 +48816,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Naumov, Vladimir A., et al. ""Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips."" Epigenetics 8.9 (2013): 0-1. PMID: 23867710 + Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48812,7 +48831,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Polidoro, Silvia, et al. ""Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw."" Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 + Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48827,7 +48846,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Edwards, Todd L., et al. ""Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease."" Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 + Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48848,7 +48867,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Vissers, Lisenka ELM, et al. ""A de novo paradigm for mental retardation."" Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 + Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48890,7 +48909,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Wartman, Lukas D., et al. ""Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression."" The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 + Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48932,7 +48951,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Filges, Isabel, et al. ""Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome."" Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 + Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48953,7 +48972,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Spaethling, Jennifer M., and James H. Eberwine. ""Single-cell transcriptomics for drug target discovery."" Current opinion in pharmacology (2013). pmid:23725882 + Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg @@ -48974,10 +48993,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - Kolbert, Christopher P., et al. ""Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues."" PloS one 8.1 (2013): e52517. PMID:23382819 + Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. - PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed ""V2"" per https://github.com/obi-ontology/obi/issues/831 on 20180511. + PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed "V2" per https://github.com/obi-ontology/obi/issues/831 on 20180511. https://www.nanostring.com/products/mirna-assays/mirna-panels nCounter Human miRNA Expression array @@ -51475,13 +51494,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - + @@ -51493,7 +51506,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - A B cell epitope assay that measures the on rate using a bio-layer interferometry assay. + A bio-layer interferometry assay that measures the on rate of a B cell epitope. IEDB IEDB on rate|bio-layer interferometry assay|M^-1s^-1 @@ -51505,13 +51518,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - + @@ -51523,7 +51530,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - A B cell epitope assay that measures the off rate using a bio-layer interferometry assay. + A bio-layer interferometry assay that measures the off rate of a B cell epitope. IEDB IEDB off rate|bio-layer interferometry assay|1/s @@ -51535,14 +51542,8 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - A B cell epitope qualitative binding to antibody assay that uses a bio-layer interferometry assay. + + A bio-layer interferometry assay that detects a B cell epitope qualitative binding to antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|bio-layer interferometry assay @@ -51554,13 +51555,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - + @@ -51572,7 +51567,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a bio-layer interferometry assay. + A bio-layer interferometry assay that measures the dissociation constant [KD] of a B cell epitope binding. IEDB IEDB dissociation constant KD|bio-layer interferometry assay|nM @@ -53113,7 +53108,7 @@ https://www.doi.org/ - + @@ -58484,12 +58479,6 @@ https://www.doi.org/ - - - - - - A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios @@ -58578,7 +58567,7 @@ https://www.doi.org/ - Kolbert, Christopher P., et al. ""Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues."" PloS one 8.1 (2013): e52517. PMID:23382819 + Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 @@ -59837,7 +59826,7 @@ https://www.doi.org/ Illumina NovaSeq 6000 - ""Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system."" + Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. Dan Berrios NovaSeq 6000 @@ -59884,7 +59873,7 @@ https://www.doi.org/ PacBio Sequel II The cDNAs were sequenced on the PacBio Sequel II platform. - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (""HiFi"") long reads, and which is manufactured by the Pacific Biosciences corporation. + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. Bonita Lam Dan Berrios Pacific BioSciences Sequel II @@ -60299,7 +60288,7 @@ https://www.doi.org/ - + @@ -60501,6 +60490,7 @@ https://www.doi.org/ A biopsy involving a surgical incision into an organism to access the biopsy material. Damion Dooley + excisional biopsy open biopsy https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 surgical biopsy @@ -62598,7 +62588,7 @@ https://www.doi.org/ - + @@ -62616,7 +62606,7 @@ https://www.doi.org/ - An assay that aims to detect pathogens. + An organism identification assay that aims to detect pathogens. VEuPathDB pathogen detection method IRO:0000137 @@ -63708,7 +63698,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A specimen that is collected with a suctioning tube from the trachea. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 tracheal wash specimen PMID:25338241 tracheal aspirate specimen @@ -63745,7 +63735,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 mid-turbinate nasal swab specimen @@ -63781,9 +63771,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A specimen that is collected with a suctioning tube from the nasal cavity. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal wash specimen|nasopharyngeal aspirate - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal aspirate specimen @@ -63818,9 +63808,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A specimen that is collected with a suctioning tube from the lower respiratory tract. - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract wash specimen - Asiyah Yu Lin|ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract aspirate specimen @@ -63855,8 +63845,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 upper respiratory specimen @@ -63891,8 +63881,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract specimen @@ -63927,8 +63917,8 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 + Asiyah Yu Lin ORCID:0000-0003-2620-0345 anterior nasal swab specimen @@ -64355,7 +64345,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - protective apron @@ -64834,7 +64823,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A device designed to catch arthropods. John Judkins - trap catch MIRO:30000011 https://github.com/obi-ontology/obi/issues/1217 arthropod trap @@ -64873,7 +64861,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -64893,7 +64880,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -64913,7 +64899,6 @@ 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 IRO:0000028 VSMO:0001906 https://github.com/obi-ontology/obi/issues/1217 @@ -64926,9 +64911,10 @@ 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 light attractant. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. + 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 + CDC light trap IRO:0000163 https://github.com/obi-ontology/obi/issues/1217 Centers for Disease Control and Prevention light trap @@ -64956,7 +64942,7 @@ 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 + EVS trap IRO:0000029 VSMO:0001295 https://github.com/obi-ontology/obi/issues/1217 @@ -64971,7 +64957,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -64985,7 +64970,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -64999,7 +64983,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A light trap designed to be placed inside a building. John Judkins - indoor light trap catch + indoor light trap MIRO:30000009 https://github.com/obi-ontology/obi/issues/1217 light trap for indoor use @@ -65013,7 +64997,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre A light trap designed to be placed outside a building. John Judkins - outdoor light trap catch + outdoor light trap MIRO:30000010 https://github.com/obi-ontology/obi/issues/1217 light trap for outdoor use @@ -65027,7 +65011,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 @@ -65054,7 +65037,7 @@ 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 light attractant. John Judkins - new jersey trap catch + New Jersey trap IRO:0000031 https://github.com/obi-ontology/obi/issues/1217 New Jersey light trap @@ -65083,7 +65066,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + outlet window trap MIRO:30000020 https://github.com/obi-ontology/obi/issues/1217 outlet window trap @@ -65202,287 +65185,940 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + + - - - - - - - - - - - - - + + + + - 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 + + + + + + + + + + + + + + + + + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/1 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based apoptosis assay - + - + + - - - - - - - - - - - - - + + + + - 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 + + + + + + + + + + + + + + + + + A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + fluroescence imaging-based cell count assay + url:http://lincsportal.ccs.miami.edu/beta/assays/31 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell proliferation assay - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/10 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluroescence imaging-based cell cycle state assay - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/27 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell viability assay - + - - - When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence being analyzed is the input gene sequence start site. - The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). - Emma Griffiths - input gene start - query gene start site - Emma Griffiths - input gene sequence start site + + + + + + + + + + + + + + + + + + + + + + + + + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/7 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based drug synergy assay - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based cell morphology assay - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/8 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging multiplex cytological profiling - + - - - 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 + + + A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + protein state assay - + - - - 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 + + + + + + + + + + + + + + + + + + + + + + + + + A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:http://lincsportal.ccs.miami.edu/beta/assays/15 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based protein phosphorylation state assay - + - - - 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 + + + + + + + + + A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + mass spectrometry-based protein state assay - + - - - 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 + + + A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + P100 phosphoprotein quantification assay + PMID:26912667 + PMID:29655704 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay - + - - - 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 + + + A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + RPLA assay + RPPA assay + reverse phase lysate array profiling assay + PMID: 17041095 + PMID:31820393 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + reverse phase protein array profiling assay - + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + - An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. + A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. + Michelle Giglio Rebecca Jackson - MRI - url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging - https://github.com/obi-ontology/obi/issues/1290 - magnetic resonance imaging assay + Suvarna Nadendla + sequential window acquisition of all theoretical mass spectra protein profiling assay + PMID:30104418 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + SWATH-MS protein profiling assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. + + + A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. + Michelle Giglio 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 + Suvarna Nadendla + PMID:12713048 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + tandem mass tag mass spectrometry - + - + + + + + + + + + + + + + + + + + + + + + + + + + A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + fluorescence imaging-based reporter gene assay + + + + + + + + + + + + + + + + + + + + + A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + GCP + global chromatin epigenetic profiling + global chromatin profiling + PMID:25448295 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + global chromatin profiling by mass spectrometry assay + + + + + + + + + A type of assay that identifies compounds that inhibit the activity of kinases. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CFDE + Michelle Giglio + Suvarna Nadendla + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + kinase inhibitor assay + + + + + + + + + A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.discoverx.com/technologies-platforms/competitive-binding-technology/kinomescan-technology-platform + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + KINOMEscan assay + + + + + + + + + A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.kinativ.com/technology.html + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + KiNativ assay + + + + + + + + + A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + L1000 mRNA profiling assay + PMID:29195078 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + landmark transcript profiling assay + + + + + + + + + A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + MEMA assay + PMID:29199020 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + microenvironment microarray assay + + + + + + + + + A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:28092050 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + microwestern meso-scale quantitative western blot assay + + + + + + + + + + + + + + + A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + positive/negative ion switching metabolomic assay + PMID:22498707 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + positive/negative ion switching metabolite profiling assay + + + + + + + + + A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + PMID:27925668 + PMID:29993362 + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + cyclic immunoflouroescence assay + + + + + + + + + A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + url:https://www.bio-rad.com/en-us/applications-technologies/multiplex-immunoassays?ID=LUSM0E8UU + https://github.com/obi-ontology/obi/issues/1243 + CFDE-LINCS + multiplex bead-based protein state immunoassay + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + + + 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 + + + + + + + @@ -65796,7 +66432,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre VSMO:0001355 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB - device for resting of adult arthropods for collection + device for collection of resting adult arthropods @@ -66422,6 +67058,1230 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + barcode target locus role + An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. + Chris Stoeckert https://orcid.org/0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1325 + barcode target locus role + + + + + + + + + + + + + + + oligonucleotide primer set + A processed material that consists of oligonucleotides that bear a primer role. + Chris Stoeckert https://orcid.org/0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1325 + oligonucleotide primer set + + + + + + + + + A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. + John Judkins + TaqMan + MIRO:20000102 + https://github.com/obi-ontology/obi/issues/1320 + fluorogenic PCR assay + + + + + + + + + + + + + + + genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci. + A genotyping assay that uses polymerase chain reaction. + Chris Stoeckert, ORCID:0000-0002-5714-991X + Jie Zheng, ORCID:0000-0002-2999-0103 + VEuPathDB + https://github.com/obi-ontology/obi/issues/1348 + VEuPathDB + genotyping by PCR assay + + + + + + + + + A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CUT&RUN assay + url:https://elifesciences.org/articles/21856 + https://github.com/obi-ontology/obi/issues/1192 + bonitalam + cleavage under targets and release using nuclease assay + + + + + + + + + A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. + Michelle Giglio + Rebecca Jackson + Suvarna Nadendla + CUT&Tag assay + url:https://www.nature.com/articles/s41467-019-09982-5 + https://github.com/obi-ontology/obi/issues/1192 + bonitalam + cleavage under targets and tagmentation + + + + + + + + + Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. + A physical examination of individual that has the objective to determine the severity of coma in a patient. + John Judkins + https://github.com/obi-ontology/obi/issues/1357 + John Judkins + coma severity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assay that detects Plasmodium gametocytes in a specimen. + Chris Stoeckert + Jie Zheng + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + Plasmodium gametocyte detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. + Chris Stoeckert + Jie Zheng + malaria rapid diagnosis test + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + malaria rapid diagnosis assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assay that detects parasite in a specimen. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assay that detects microorganisms in a feces specimen. + John Judkins + stool test for microorganisms + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + feces microbiology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assay that has a blood specimen as evaulant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + blood assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + falcivax rapid diagnostic test + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + optimal-IT rapid diagnostic test + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assay that has a urine specimen as evaluant. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + urine assay + + + + + + + + + + + + + + + An organism identification assay that identifies the species of parasites by PCR. + John Judkins + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite species identification by PCR assay + + + + + + + + + + + + + + + + + + + + + An assay that detects parasite in a specimen using PCR. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + parasite detection by PCR assay + + + + + + + + + Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658] + An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die. + VEuPathDB + VSMO:0001649 + free-standing window trap + + + + + + + + + + + + + + + A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin. + VEuPathDB + BG-lure + IRO:0001060 + BG-lure scent dispenser + + + + + + + + + A device that consists of a network of mesh and is designed to capture adult arthropods. + VEuPathDB + VSMO:0001522 + hand-held sweep net + + + + + + + + + The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658] + A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan. + VEuPathDB + CDC gravid trap + VSMO:0001510 + Centers for Disease Control and Prevention gravid trap + + + + + + + + + An arthropod specimen collection process in which the arthropods are in the embryo stage. + VEuPath + collection of eggs + MIRO:30000049 + https://github.com/obi-ontology/obi/issues/1322 + egg specimen collection process + + + + + + + + + An arthropod specimen collection process in which the arthropods are in the larval stage. + VEuPath + collection of larvae + MIRO:30000022 + https://github.com/obi-ontology/obi/issues/1322 + larval specimen collection process + + + + + + + + + An arthropod specimen collection process in which the arthropods are in the pupal stage. + VEuPath + collection of pupae + MIRO:30000050 + https://github.com/obi-ontology/obi/issues/1322 + pupal specimen collection process + + + + + + + + + + + + + + + + + + + + + + + A blood specimen that is located in a vacutainer. + John Judkins + Vacutainer sample + VEuPathDB + blood specimen in vacutainer + + + + + + + + + + + + + + + + + + + + + + + A blood specimen that is located on a filter paper. + Chris Stoeckert + Jie Zheng + Filter paper sample + Penn Group + blood specimen on filter paper + + + + + + + + + A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads. + John Judkins + VEuPathDB + proportion mapped reads + + + + + + + + + + + + + + + + + + + + + + + + + Administering substance in vivo where an antibiotic substance is administered to a living organism. + Chris Stoeckert + Cristian Cocos + Jie Zheng + Penn Group + antibiotic administration process + + + + + + + + + A data item that is about resistance to an insecticide. + John Judkins + VEuPathDB + insecticide resistance datum + + + + + + + + + A data item that is the specified output of an organism identification assay. + John Judkins + VEuPathDB + organism identification datum + + + + + + + + + A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. + Easting and northing coordinates are commonly measured in meters from a horizontal datum. + John Judkins + https://en.wikipedia.org/wiki/Grid_reference_system + easting coordinate measurement datum + + + + + + + + + A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. + Easting and northing coordinates are commonly measured in meters from a horizontal datum. + John Judkins + https://en.wikipedia.org/wiki/Grid_reference_system + northing coordinate measurement datum + + + + + + + + + Organization that undertakes a clinical study at some point in time. + Chris Stoeckert + Cristian Cocos + Jie Zheng + Penn Group + clinical study center + + + + + + + + + A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. + John Judkins + VEuPathDB + sequencing protocol + + + + + + + + + + + + + + + A protocol that specifies processes to fulfill a specimen collection objective. + John Judkins + VEuPathDB + specimen collection protocol + + + + + + + + + + + + + + + + + + + + + + + + + A symbol that denotes a participant under investigation. + John Judkins + VEuPathDB + participant identifier + + + + + + + + + A temperature measurement datum that is about an axilla. + John Judkins + VEuPathDB + axillary temperature measurement datum + + + + + + + + + A temperature measurement datum that is about an organism. + Chris Stoeckert + Jie Zheng + Penn Group + organismal body temperature measurement datum + + + + + + + + + + + + + + + A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized. + John Judkins + https://en.wikipedia.org/wiki/Common_name + common name of organism + + + + + + + + + An age since birth measurement datum at the time of subject enrollment. + Jie Zheng + Penn Group + age since birth at time of enrollment + + + + + + + + + An age since birth measurement datum at the time of a clinical visit. + Chris Stoeckert + Grant Dorsey + Jie Zheng + Shon Cade + Penn Group + age since birth at time of visit + + + + + + + + + A data item that is about a collection of insects. + John Judkins + entomological measurement datum + VEuPathDB + entomological data item + + + + + + + + + A scalar measurement datum that is the result of measuring temperature. + John Judkins + VEuPathDB + temperature measurement datum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An assay that detects body temperature of an organism. + Chris Stoeckert + Jie Zheng + VEuPathDB + https://github.com/obi-ontology/obi/issues/1322 + organismal body temperature measurement assay + + + + + + + + + extraction date + A time measurement datum that specifies when some material was extracted from an input material. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + FLU, VEuPathDB + https://github.com/obi-ontology/obi/issues/1286 + extraction date + + + + + + + + + extraction duration time + A time measurement datum that is the result of measuring the duration of an extraction process. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + Meredith Keybl, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + extraction duration time + + + + + + + + + specimen collection time post disease onset + A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + GROUP:FLU, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + specimen collection time post disease onset + + + + + + + + + specimen collection time post infection + A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + VEuPathDB, EUPATH:0000613 + https://github.com/obi-ontology/obi/issues/1286 + specimen collection time post infection + + + + + + + + + laboratory postal address + A postal address used as a directive to deliver something to a laboratory. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + laboratory address + GROUP:FLU, Shane Babcock + https://github.com/obi-ontology/obi/issues/1286 + laboratory postal address + + + + + + + + + laboratory-based population + Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033) + A population where the collection of individuals is located and maintained in a laboratory, research, or production facility. + Chris Stoeckert, ORCID: 0000-0002-5714-991X + VEuPathDB + https://github.com/obi-ontology/obi/issues/1370 + laboratory-based population + + + + + + + + + + + + + + + Illumina MiniSeq + Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526 + A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + PERSON: Bonita Lam + MiniSeq + url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html + Illumina MiniSeq + + + + @@ -66497,7 +68357,9 @@ b) that the amount of analyte/measurand detected is over some predetermined thre 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 + Bjoern Peters + Philippe Rocca-Serra + Tina Boussard MO obsolete_anatomical entity @@ -66766,7 +68628,8 @@ This issue is outside the scope of OBI. 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 + immortal cell line sample + permanent cell line PERSON:Matthew Brush @@ -66899,7 +68762,8 @@ A cultured cell population maintained in vitro: "Rat cortical neurons from - A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line". Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592.|He, Tong-Chuan, et al. "Identification of c-MYC as a target of the APC pathway." Science 281.5382 (1998): 1509-1512. - "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'." + 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 @@ -67049,7 +68913,8 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ 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 + James Malone + Philippe Rocca-Serra TERM: CHEBI:33839 obsolete_polymer @@ -71077,8 +72942,8 @@ determinations of compounds. a collection is a bfo:aggregate object, that is a set of material object of the same kind PERSON: Susanna Sansone - ensemble - group + ensemble + group set PERSON: Philippe Rocca-Serra @@ -71426,8 +73291,7 @@ determinations of compounds. - PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. -AJR Am J Roentgenol. 1990 Jan;154(1):87-93. + 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 @@ -72132,8 +73996,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63. - a process by which a material entity status is modified and conferred a capability of reacting -(this sounds like a circular definition , hugh!) + 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 @@ -72874,11 +74737,11 @@ Manual editing of automatically recorded data in an anesthesia information manag FACS Calibur - ""FACS Calibur at TFL, BCCRC, Vancouver"" + 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"" + http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11 FACS Calibur @@ -73857,7 +75720,7 @@ Manual editing of automatically recorded data in an anesthesia information manag 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"" + http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10 SomaScope @@ -74468,7 +76331,7 @@ Manual editing of automatically recorded data in an anesthesia information manag 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. + 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 @@ -74681,7 +76544,7 @@ Manual editing of automatically recorded data in an anesthesia information manag DNA microarray - Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). ""Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis"". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115 + 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 @@ -80958,8 +82821,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some uterine cervix - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 uterine cervix specimen @@ -80988,8 +82853,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 urethra specimen @@ -81018,8 +82885,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some cervical mucus - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 cervical mucus specimen @@ -81048,8 +82917,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 throat specimen @@ -81078,8 +82949,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 eye specimen @@ -81108,8 +82981,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some respiratory system - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 respiratory system specimen @@ -81138,8 +83013,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some upper respiratory tract - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 upper respiratory tract specimen @@ -81168,8 +83045,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 nasopharynx specimen @@ -81198,8 +83077,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 semen specimen @@ -81228,8 +83109,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some bodily fluid - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 bodily fluid specimen @@ -81258,8 +83141,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some chorionic villus - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 chorionic villus specimen @@ -81288,8 +83173,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 meconium specimen @@ -81318,8 +83205,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some umbilical cord blood - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 umbilical cord blood specimen @@ -81348,8 +83237,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some arterial blood - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 arterial blood specimen @@ -81378,8 +83269,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some venous blood - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 venous blood specimen @@ -81408,8 +83301,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 A specimen that is derived from some capillary blood - 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 capillary blood specimen @@ -81440,8 +83335,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 erythrocyte specimen @@ -81472,8 +83369,10 @@ 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 reticulocyte specimen @@ -81504,8 +83403,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 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 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 + Christian Stoeckert ORCID:0000-0002-5714-991X + Mark A. Miller ORCID:0000-0001-9076-6066 leukocyte specimen @@ -102938,7 +104839,78 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + + + + + + + + + + + + + + An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + liver function venous blood human aspartate aminotransferase assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -102946,23 +104918,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order + 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 human aspartate aminotransferase assay + liver function venous blood albumin assay - + - + @@ -103009,7 +104981,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103017,23 +104989,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order + 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 albumin assay + liver function venous blood protein assay - + - + @@ -103080,7 +105052,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103088,23 +105060,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of protein in venous blood as part of a liver function order + 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 protein assay + liver function venous blood human alkaline phosphatase assay - + - + @@ -103151,7 +105123,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103159,24 +105131,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order + 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 - liver function venous blood human alkaline phosphatase assay + vitamin B12 and Folate venous blood folic acid assay - + - - + + @@ -103188,7 +105160,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103199,7 +105171,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103211,6 +105183,30 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + + + + + + + + + + + + A cytometry assay that measures the count of cells in bodily fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + bodily fluid cell count assay + + + + + + + + @@ -103219,10 +105215,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - - + + @@ -103230,24 +105226,45 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + + + + + + + + + + + - An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order + + + + + + + + + + + + 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 - vitamin B12 and Folate venous blood folic acid assay + venous blood reticulocyte count assay - + - - + + @@ -103283,29 +105300,42 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - A cytometry assay that measures the count of cells in bodily fluid + 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 cell count assay + bodily fluid cholesterol assay - + - - + + @@ -103341,28 +105371,41 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - A cytometry assay that measures the count of reticulocytes in venous blood + 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 - venous blood reticulocyte count assay + TSH reflex Free T4 venous blood thyroid stimulating hormone assay - + - + @@ -103375,7 +105418,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103386,7 +105429,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103409,7 +105452,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103417,23 +105460,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of cholesterol in bodily fluid + 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 - bodily fluid cholesterol assay + direct venous blood bilirubin assay - + - + @@ -103480,7 +105523,78 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + + + + + + + + + + + + + + An analyte assay that measures the abundance of T3 in venous blood as part of a free order + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + free venous blood T3 assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -103488,23 +105602,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order + 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 - TSH reflex Free T4 venous blood thyroid stimulating hormone assay + bodily fluid albumin assay - + - + @@ -103517,7 +105631,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103528,7 +105642,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103551,7 +105665,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103559,24 +105673,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order + 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 - direct venous blood bilirubin assay + bodily fluid triglyceride assay - + - - + + @@ -103612,41 +105726,28 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - An analyte assay that measures the abundance of T3 in venous blood as part of a free order + 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 - free venous blood T3 assay + hemoglobin and hematocrit venous blood hematocrit assay - + - + @@ -103659,7 +105760,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103670,7 +105771,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103693,7 +105794,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103701,23 +105802,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of albumin in bodily fluid + 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 - bodily fluid albumin assay + hemoglobin and hematocrit venous blood hemoglobin assay - + - + @@ -103730,7 +105831,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103741,7 +105842,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103764,7 +105865,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103772,24 +105873,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of triglyceride in bodily fluid + 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 - bodily fluid triglyceride assay + venous blood ionized calcium assay - + - - + + @@ -103830,23 +105931,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order + 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 - hemoglobin and hematocrit venous blood hematocrit assay + venous blood temperature assay - + - + @@ -103893,7 +105994,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103901,23 +106002,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order + 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 - hemoglobin and hematocrit venous blood hemoglobin assay + venous blood bicarbonate assay - + - + @@ -103964,7 +106065,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -103972,23 +106073,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of ionized calcium in venous blood + 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 ionized calcium assay + venous blood oxygen assay - + - + @@ -104030,24 +106131,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An assay that measures temperature in venous blood + 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 temperature assay + venous blood osmolality assay - + - - + + @@ -104083,41 +106184,28 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - An analyte assay that measures the abundance of bicarbonate in venous blood + 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 - venous blood bicarbonate assay + liver fibrosis (chronic viral hepatitis) venous blood platelet count assay - + - + @@ -104164,7 +106252,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104172,24 +106260,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of oxygen in venous blood + 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 oxygen assay + venous blood T3 assay - + - - + + @@ -104230,24 +106318,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An assay that measures osmolality in venous blood + 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 - venous blood osmolality assay + CBC with manual differential venous blood neutrophil count assay - + - - + + @@ -104259,7 +106347,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104270,7 +106358,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104283,28 +106371,41 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order + 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 - liver fibrosis (chronic viral hepatitis) venous blood platelet count assay + creatinine clearance urine creatinine assay - + - + @@ -104351,7 +106452,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104359,23 +106460,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of T3 in venous blood + 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 T3 assay + venous blood beta hydroxybutryic acid assay - + - + @@ -104417,24 +106518,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order + 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 - CBC with manual differential venous blood neutrophil count assay + venous blood megakaryocyte count assay - + - - + + @@ -104446,7 +106547,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104457,7 +106558,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104470,42 +106571,29 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order + 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 - creatinine clearance urine creatinine assay + venous blood nucleated RBC count assay - + - - + + @@ -104541,41 +106629,28 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood + 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 beta hydroxybutryic acid assay + venous blood WBC count assay - + - + @@ -104617,24 +106692,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - A cytometry assay that measures the count of megakaryocytes in venous blood + 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 - venous blood megakaryocyte count assay + automated count venous blood reticulocyte count assay - + - - + + @@ -104670,29 +106745,42 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - A cytometry assay that measures the count of nucleated RBCs in venous blood + 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 - venous blood nucleated RBC count assay + total venous blood homocysteine assay - + - - + + @@ -104728,29 +106816,42 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - A cytometry assay that measures the count of WBCs in venous blood + 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 WBC count assay + venous blood Ceruloplasmin assay - + - - + + @@ -104762,7 +106863,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104773,7 +106874,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104786,29 +106887,42 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order + 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 - automated count venous blood reticulocyte count assay + GEM4 arterial blood bicarbonate assay - + - - + + @@ -104820,7 +106934,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104831,7 +106945,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104844,41 +106958,28 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order + 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 - total venous blood homocysteine assay + GEM4 arterial blood lactic acid assay - + - + @@ -104891,7 +106992,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104902,7 +107003,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104925,7 +107026,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -104933,23 +107034,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of Ceruloplasmin in venous blood + 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 - venous blood Ceruloplasmin assay + GEM4 arterial blood hemoglobin assay - + - + @@ -104996,7 +107097,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105004,24 +107105,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order + 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 bicarbonate assay + GEM4 arterial blood sodium assay - + - - + + @@ -105057,29 +107158,42 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - An assay that measures lactic acid in arterial blood as part of a GEM4 order + 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 lactic acid assay + GEM4 arterial blood potassium assay - + - - + + @@ -105115,41 +107229,28 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - + + + - - + + - - + + - An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order + 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 hemoglobin assay + GEM4 arterial blood temperature assay - + - + @@ -105196,7 +107297,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105204,23 +107305,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order + 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 sodium assay + GEM4 arterial blood glucose assay - + - + @@ -105267,7 +107368,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105275,24 +107376,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order + 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 potassium assay + GEM4 arterial blood oxygen assay - + - - + + @@ -105333,23 +107434,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An assay that measures temperature in arterial blood as part of a GEM4 order + 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 temperature assay + GEM4 arterial blood hematocrit assay - + - + @@ -105396,7 +107497,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105404,23 +107505,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order + 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 glucose assay + GEM4 arterial blood ionized calcium assay - + - + @@ -105467,7 +107568,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105475,23 +107576,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order + 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 oxygen assay + GEM4 arterial blood carbon dioxide assay - + - + @@ -105504,7 +107605,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105515,7 +107616,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105533,94 +107634,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - GEM4 arterial blood hematocrit assay - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order + 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 - GEM4 arterial blood ionized calcium assay + liver fibrosis (NAFLD) venous blood platelet count assay - + - + @@ -105633,7 +107663,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105644,7 +107674,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105667,7 +107697,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105675,23 +107705,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order + 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 - GEM4 arterial blood carbon dioxide assay + venous blood beta hydroxybutric acid assay - + - + @@ -105733,23 +107763,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order + 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 - liver fibrosis (NAFLD) venous blood platelet count assay + CBC with manual differential venous blood plasma cell count assay - + - + @@ -105796,7 +107826,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105804,24 +107834,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood + 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 beta hydroxybutric acid assay + venous blood erythropoietin assay - + - - + + @@ -105833,7 +107863,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105844,7 +107874,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105857,28 +107887,41 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - + + - - + + + + + + + + + + + + - - + + + + + + - A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order + 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 - CBC with manual differential venous blood plasma cell count assay + blood gas arterial blood oxygen assay - + - + @@ -105891,7 +107934,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105902,7 +107945,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105925,7 +107968,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -105933,23 +107976,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of erythropoietin in venous blood + 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 - venous blood erythropoietin assay + blood gas arterial blood bicarbonate assay - + - + @@ -105996,7 +108039,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106004,23 +108047,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order + 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 oxygen assay + blood gas arterial blood carbon dioxide assay - + - + @@ -106033,7 +108076,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106044,7 +108087,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106067,7 +108110,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106075,24 +108118,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order + 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 - blood gas arterial blood bicarbonate assay + free/total venous blood PSA assay - + - - + + @@ -106104,7 +108147,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106115,7 +108158,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106127,6 +108170,30 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + + + + + + + + + + + + A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid lymphocyte count assay + + + + + + + + @@ -106135,10 +108202,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - - + + @@ -106146,24 +108213,45 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + + + + + + + + + + + - An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order + + + + + + + + + + + + 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 - blood gas arterial blood carbon dioxide assay + cerebrospinal fluid segmented neutrophil count assay - + - - + + @@ -106175,7 +108263,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106186,7 +108274,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106198,6 +108286,30 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 + + + + + + + + + + + + A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid + Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X + PennTURBO team + https://github.com/obi-ontology/obi/issues/1253 + cerebrospinal fluid mesothelial cell count assay + + + + + + + + @@ -106206,10 +108318,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - - + + @@ -106217,23 +108329,44 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + + + + + + + + + + + - An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order + + + + + + + + + + + + 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 - free/total venous blood PSA assay + cerebrospinal fluid macrophage count assay - + - + @@ -106275,23 +108408,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid + 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 lymphocyte count assay + cerebrospinal fluid basophil count assay - + - + @@ -106333,23 +108466,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid + 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 segmented neutrophil count assay + cerebrospinal fluid monocyte count assay - + - + @@ -106391,24 +108524,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid + 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 mesothelial cell count assay + cerebrospinal fluid eosinophil count assay - + - - + + @@ -106420,7 +108553,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106431,7 +108564,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106443,30 +108576,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - A cytometry assay that measures the count of macrophages in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid macrophage count assay - - - - - - - - @@ -106475,10 +108584,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - - + + @@ -106486,45 +108595,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - + - - - - - - - - - - - - A cytometry assay that measures the count of basophils in cerebrospinal fluid + 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 - cerebrospinal fluid basophil count assay + venous blood beta-2-microglobulin assay - + - - + + @@ -106536,7 +108624,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106547,7 +108635,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106559,30 +108647,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - A cytometry assay that measures the count of monocytes in cerebrospinal fluid - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - cerebrospinal fluid monocyte count assay - - - - - - - - @@ -106591,10 +108655,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - - + + @@ -106602,44 +108666,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - + - - - - - - - - - - - - A cytometry assay that measures the count of eosinophils in cerebrospinal fluid + 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 - cerebrospinal fluid eosinophil count assay + lipid panel reflex direct venous blood low density lipoprotein assay - + - + @@ -106686,7 +108729,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106694,23 +108737,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of beta-2-microglobulin in venous blood + 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 - venous blood beta-2-microglobulin assay + lipid panel reflex direct venous blood triglyceride assay - + - + @@ -106757,7 +108800,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106765,23 +108808,23 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order + 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 low density lipoprotein assay + lipid panel reflex direct venous blood cholesterol assay - + - + @@ -106828,7 +108871,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106836,58 +108879,24 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order + 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 triglyceride assay + lipid panel reflex direct venous blood high density lipoprotein assay - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -106896,10 +108905,10 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - + @@ -106907,24 +108916,11 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + - An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel reflex direct venous blood cholesterol assay - - - - - - - - @@ -106936,7 +108932,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106947,7 +108943,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + @@ -106960,34 +108956,18 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - - - - - - - - - - - - - - - - - - + + + + - An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order - Mark A. Miller, ORCID:0000-0001-9076-6066 & Chris Stoeckert, ORCID ORCID:0000-0002-5714-991X - PennTURBO team - https://github.com/obi-ontology/obi/issues/1253 - lipid panel reflex direct venous blood high density lipoprotein assay + Although a similar pooled clone sequencing method has recently been described by others for metagenome-derived medium-insert plasmids and large-insert fosmids, to our knowledge, we are the first to report the pooled strategy for sequencing of large-insert metagenomic clones while also critically evaluating the performance of this pooled strategy by comparing the results to barcoded reference sequences of the same clones. + A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced. + Dan Berrios, ORCID: 0000-0003-4312-9552 + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049660/ + https://github.com/obi-ontology/obi/issues/1106 + Bonita Lam + pooled clone sequencing assay @@ -107083,6 +109063,18 @@ realizes some 'host of immune response role' + + + + + + + + + + + + @@ -108925,12 +110917,6 @@ realizes some 'host of immune response role' - - - - - - right handed right handed @@ -108941,12 +110927,6 @@ realizes some 'host of immune response role' - - - - - - ambidexterous ambidexterous @@ -108957,12 +110937,6 @@ realizes some 'host of immune response role' - - - - - - left handed left handed diff --git a/views/obi.obo b/views/obi.obo index 0e796654..a02ad5af 100644 --- a/views/obi.obo +++ b/views/obi.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: obi/2021-04-06/obi.obo -date: 06:04:2021 10:16 +data-version: obi/2021-08-18/obi.obo +date: 18:08:2021 11:00 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 @@ -48,8 +48,8 @@ property_value: http://purl.org/dc/elements/1.1/creator "Melissa Haendel" xsd:st property_value: http://purl.org/dc/elements/1.1/creator "Mervi Heiskanen" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Monnie McGee" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Norman Morrison" xsd:string -property_value: http://purl.org/dc/elements/1.1/creator "Philip Lord" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Philippe Rocca-Serra" xsd:string +property_value: http://purl.org/dc/elements/1.1/creator "Phillip Lord" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Pierre Grenon" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Richard Bruskiewich" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Richard Scheuermann" 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 "2021-04-06" xsd:string +property_value: owl:versionInfo "2021-08-18" xsd:string [Term] id: APOLLO_SV:00000008 @@ -3459,6 +3459,12 @@ name: pathogen def: "A material entity with a pathogenic disposition." [] is_a: BFO:0000040 ! material entity +[Term] +id: IDO:0000562 +name: antibacterial +def: "A material entity bearing an antibacterial disposition." [] +is_a: BFO:0000040 ! material entity + [Term] id: IDO:0000586 name: infection @@ -3507,31 +3513,59 @@ id: NCBITaxon:10376 name: Human gammaherpesvirus 4 synonym: "Epstein Barr virus" EXACT [] synonym: "Epstein-Barr virus" EXACT [] +synonym: "Epstein-Barr virus EBV" EXACT [] +synonym: "Human herpesvirus 4" EXACT [] +synonym: "Human herpesvirus type 4" EXACT [] is_a: NCBITaxon:10292 ! Herpesviridae [Term] id: NCBITaxon:10407 name: Hepatitis B virus -is_a: NCBITaxon:10239 ! Viruses +synonym: "hepatitis B virus (HBV)" EXACT [] +synonym: "hepatitis B virus HBV" EXACT [] +synonym: "hepatitis B virus, HBV" EXACT [] +synonym: "Human hepatitis B virus" EXACT [] +synonym: "human hepatitis B virus HBV" EXACT [] +is_a: NCBITaxon:2732514 ! Revtraviricetes [Term] id: NCBITaxon:11103 name: Hepacivirus C -is_a: NCBITaxon:10239 ! Viruses +synonym: "Hepatitis C virus" EXACT [] +synonym: "hepatitis C virus HCV" EXACT [] +synonym: "human hepatitis C virus" EXACT [] +synonym: "human hepatitis C virus HCV" EXACT [] +synonym: "human hepatitis virus C HCV" EXACT [] +synonym: "post-transfusion hepatitis non A non B virus" EXACT [] +is_a: NCBITaxon:2559587 ! Riboviria [Term] id: NCBITaxon:11646 name: Lentivirus -is_a: NCBITaxon:10239 ! Viruses +synonym: "Lentivirinae" EXACT [] +is_a: NCBITaxon:2732514 ! Revtraviricetes [Term] id: NCBITaxon:11676 name: Human immunodeficiency virus 1 +synonym: "human immunodeficiency virus 1 HIV-1" EXACT [] +synonym: "human immunodeficiency virus HIV-1" EXACT [] +synonym: "human immunodeficiency virus type 1 HIV 1" EXACT [] +synonym: "human immunodeficiency virus type 1 HIV1" EXACT [] +synonym: "human immunodeficiency virus type 1, HIV-1" EXACT [] +synonym: "human immunodeficiency virus type I HIV-1" EXACT [] +synonym: "human immunodeficiency virus type-1 HIV-1" EXACT [] +synonym: "human immunodeficiency virus-1 HIV-1" EXACT [] is_a: NCBITaxon:11646 ! Lentivirus [Term] id: NCBITaxon:11709 name: Human immunodeficiency virus 2 +synonym: "HIV type 2" EXACT [] +synonym: "Human immunodeficiency virus type 2" EXACT [] +synonym: "human immunodeficiency virus type 2 HIV-2" EXACT [] +synonym: "human immunodeficiency virus type 2, HIV-2" EXACT [] +synonym: "Human immunodeficiency virus-2" EXACT [] is_a: NCBITaxon:11646 ! Lentivirus [Term] @@ -3553,7 +3587,7 @@ is_a: NCBITaxon:2 ! Bacteria [Term] id: NCBITaxon:197562 name: Pancrustacea -is_a: NCBITaxon:1206794 ! Ecdysozoa +is_a: NCBITaxon:6656 ! Arthropoda [Term] id: NCBITaxon:2 @@ -3566,6 +3600,18 @@ id: NCBITaxon:2157 name: Archaea is_a: OBI:0100026 ! organism +[Term] +id: NCBITaxon:2559587 +name: Riboviria +synonym: "RNA viruses" EXACT [] +synonym: "RNA viruses and viroids" EXACT [] +is_a: NCBITaxon:10239 ! Viruses + +[Term] +id: NCBITaxon:2732514 +name: Revtraviricetes +is_a: NCBITaxon:2559587 ! Riboviria + [Term] id: NCBITaxon:2759 name: Eukaryota @@ -3655,12 +3701,23 @@ id: NCBITaxon:5140 name: Neurospora is_a: NCBITaxon:716545 ! saccharomyceta +[Term] +id: NCBITaxon:5820 +name: Plasmodium +is_a: NCBITaxon:2759 ! Eukaryota + [Term] id: NCBITaxon:6239 name: Caenorhabditis elegans synonym: "roundworm" EXACT [] is_a: NCBITaxon:1206794 ! Ecdysozoa +[Term] +id: NCBITaxon:6656 +name: Arthropoda +synonym: "arthropods" EXACT [] +is_a: NCBITaxon:1206794 ! Ecdysozoa + [Term] id: NCBITaxon:6668 name: Daphnia @@ -3873,7 +3930,7 @@ is_a: BFO:0000040 ! material entity [Term] id: OBI:0000048 name: chromatography device -def: "A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a \"\"mobile phase\"\" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated." [] +def: "A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a \"mobile phase\" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated." [] synonym: "chromatography instrument" EXACT [] is_a: OBI:0000832 ! measurement device is_a: OBI:0000932 ! material separation device @@ -5258,7 +5315,7 @@ is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000449 name: obsolete_defined_output -def: "This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application.\nIts children should be defined classes constructed as output of a process." [] +def: "This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true @@ -6500,8 +6557,8 @@ is_a: OBI:0000891 ! cell proliferation assay id: OBI:0000665 name: obsolete intracellular cytokine staining assay def: "The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer." [] -synonym: " ICS" EXACT [] synonym: "ICCS" EXACT [] +synonym: "ICS" EXACT [] synonym: "intracellular cytokine staining (ICS)" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true @@ -7430,7 +7487,7 @@ is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000854 -name: western blot analysis +name: western blot assay def: "An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules." [] is_a: OBI:0001978 ! immunoblot assay @@ -8521,7 +8578,7 @@ is_a: BFO:0000034 ! function [Term] id: OBI:0001037 name: obsolete_specimen fixation function -def: "A specimen \nfixation function is a function that holds or fastens an entity in a fixed position." [] +def: "A specimen fixation function is a function that holds or fastens an entity in a fixed position." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true @@ -8577,7 +8634,7 @@ is_a: OBI:0000968 ! device [Term] id: OBI:0001046 name: bioreactor -def: "A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT" [] +def: "A device or system that supports a biologically active environment." [] is_a: OBI:0001034 ! environmental control device [Term] @@ -9231,8 +9288,8 @@ is_a: OBI:0000456 ! material transformation objective [Term] id: OBI:0001154 -name: induced mutation -def: "a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation." [] +name: induced mutagenesis +def: "A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation." [] is_a: OBI:0600043 ! genetic transformation [Term] @@ -12567,7 +12624,7 @@ is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001669 -name: far-Western blot assay +name: far-western blot assay def: "An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay." [] is_a: OBI:0001146 ! binding assay @@ -15545,30 +15602,30 @@ is_a: OBI:0001721 ! 3D structure determining assay of a 3D B cell epitope:antibo [Term] id: OBI:0002102 name: bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex -def: "A B cell epitope assay that measures the on rate using a bio-layer interferometry assay." [] +def: "A bio-layer interferometry assay that measures the on rate of a B cell epitope. " [] synonym: "on rate|bio-layer interferometry assay|M^-1s^-1" EXACT [] -is_a: OBI:0001718 ! assay measuring the on rate [kon] of a B cell epitope:antibody complex +is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002103 name: bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex -def: "A B cell epitope assay that measures the off rate using a bio-layer interferometry assay." [] +def: "A bio-layer interferometry assay that measures the off rate of a B cell epitope." [] synonym: "off rate|bio-layer interferometry assay|1/s" EXACT [] -is_a: OBI:0001723 ! assay measuring the off rate [koff] of a B cell epitope:antibody complex +is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002104 name: bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex -def: "A B cell epitope qualitative binding to antibody assay that uses a bio-layer interferometry assay." [] +def: "A bio-layer interferometry assay that detects a B cell epitope qualitative binding to antibody." [] synonym: "qualitative binding|bio-layer interferometry assay" EXACT [] -is_a: OBI:0001703 ! assay measuring qualitiative binding of a B cell epitope:antibody complex +is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002105 name: bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex -def: "A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a bio-layer interferometry assay." [] +def: "A bio-layer interferometry assay that measures the dissociation constant [KD] of a B cell epitope binding. " [] synonym: "dissociation constant KD|bio-layer interferometry assay|nM" EXACT [] -is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex +is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002106 @@ -17889,13 +17946,13 @@ is_a: OBI:0002617 ! national registry id: OBI:0002619 name: site-directed mutagenesis def: "An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer." [] -is_a: OBI:0001154 ! induced mutation +is_a: OBI:0001154 ! induced mutagenesis [Term] id: OBI:0002620 name: random mutagenesis def: "An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR." [] -is_a: OBI:0001154 ! induced mutation +is_a: OBI:0001154 ! induced mutagenesis [Term] id: OBI:0002621 @@ -17984,7 +18041,7 @@ is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002633 name: PacBio Sequel II -def: "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"\"HiFi\"\") long reads, and which is manufactured by the Pacific Biosciences corporation." [] +def: "A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate (\"HiFi\") long reads, and which is manufactured by the Pacific Biosciences corporation." [] synonym: "Pacific BioSciences Sequel II" EXACT [] is_a: OBI:0400103 ! DNA sequencer @@ -18102,6 +18159,7 @@ id: OBI:0002649 name: blood microbiology assay def: "An organism identification assay that identifies a microorganism in a blood specimen." [] is_a: OBI:0001624 ! organism identification assay +is_a: OBI:0003040 ! blood assay [Term] id: OBI:0002650 @@ -18159,6 +18217,7 @@ is_a: OBI:0002654 ! needle biopsy id: OBI:0002657 name: surgical biopsy def: "A biopsy involving a surgical incision into an organism to access the biopsy material." [] +synonym: "excisional biopsy" EXACT [] synonym: "open biopsy" EXACT [] is_a: OBI:0002650 ! biopsy @@ -18662,9 +18721,9 @@ is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002728 name: pathogen detection assay -def: "An assay that aims to detect pathogens." [] +def: "An organism identification assay that aims to detect pathogens." [] synonym: "pathogen detection method" EXACT [] -is_a: OBI:0000070 ! assay +is_a: OBI:0001624 ! organism identification assay [Term] id: OBI:0002729 @@ -19189,7 +19248,6 @@ is_a: OBI:0002800 ! personal protective clothing item 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] @@ -19414,7 +19472,6 @@ is_a: OBI:0002913 ! arthropod specimen collection process id: OBI:0002920 name: arthropod trap def: "A device designed to catch arthropods." [] -synonym: "trap catch" EXACT [] is_a: OBI:0000968 ! device [Term] @@ -19433,28 +19490,25 @@ is_a: OBI:0002920 ! arthropod trap id: OBI:0002923 name: barrier trap def: "An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container." [] -synonym: "barrier catch" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002924 name: BG-Counter def: "A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods." [] -synonym: "BG-Counter trap catch" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0002925 name: BG-Sentinel trap def: "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." [] -synonym: "BG-Sentinel trap catch" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002926 name: Centers for Disease Control and Prevention light trap -def: "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." [] -synonym: "CDC light trap catch" EXACT [] +def: "A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant." [] +synonym: "CDC light trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] @@ -19468,42 +19522,39 @@ is_a: OBI:0000968 ! device id: OBI:0002928 name: encephalitis virus surveillance trap def: "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." [] -synonym: "EVS trap catch" EXACT [] +synonym: "EVS trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] id: OBI:0002929 name: gravid trap def: "An arthropod trap that is designed to collect gravid female arthropods or their eggs." [] -synonym: "gravid trap catch" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002930 name: light trap def: "An arthropod trap that uses light as an attractant." [] -synonym: "light trap catch" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002931 name: light trap for indoor use def: "A light trap designed to be placed inside a building." [] -synonym: "indoor light trap catch" EXACT [] +synonym: "indoor light trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] id: OBI:0002932 name: light trap for outdoor use def: "A light trap designed to be placed outside a building." [] -synonym: "outdoor light trap catch" EXACT [] +synonym: "outdoor light trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] id: OBI:0002933 name: Mosquito Magnet trap def: "An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods." [] -synonym: "mosquito magnet pro catch" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] @@ -19516,7 +19567,7 @@ is_a: OBI:0002929 ! gravid trap id: OBI:0002935 name: New Jersey light trap def: "A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant." [] -synonym: "new jersey trap catch" EXACT [] +synonym: "New Jersey trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] @@ -19530,7 +19581,7 @@ is_a: OBI:0002920 ! arthropod trap id: OBI:0002937 name: outlet window trap def: "An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building." [] -synonym: "outlet window trap catch" EXACT [] +synonym: "outlet window trap" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] @@ -19587,6 +19638,177 @@ name: population based design def: "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." [] is_a: OBI:0500000 ! study design +[Term] +id: OBI:0002946 +name: fluorescence imaging-based apoptosis assay +def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis." [] +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0002947 +name: fluorescence imaging-based cell proliferation assay +def: "A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells." [] +synonym: "fluroescence imaging-based cell count assay" EXACT [] +is_a: OBI:0000891 ! cell proliferation assay +is_a: OBI:0001501 ! fluorescence detection assay + +[Term] +id: OBI:0002948 +name: fluroescence imaging-based cell cycle state assay +def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states." [] +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0002949 +name: fluorescence imaging-based cell viability assay +def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability." [] +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0002950 +name: fluorescence imaging-based drug synergy assay +def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects." [] +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0002951 +name: fluorescence imaging-based cell morphology assay +def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology." [] +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0002952 +name: fluorescence imaging multiplex cytological profiling +def: "A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters." [] +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0002953 +name: protein state assay +def: "A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0002954 +name: fluorescence imaging-based protein phosphorylation state assay +def: "A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states." [] +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0002953 ! protein state assay + +[Term] +id: OBI:0002955 +name: mass spectrometry-based protein state assay +def: "A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states." [] +is_a: OBI:0002953 ! protein state assay + +[Term] +id: OBI:0002956 +name: targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay +def: "A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations." [] +synonym: "P100 phosphoprotein quantification assay" EXACT [] +is_a: OBI:0002955 ! mass spectrometry-based protein state assay + +[Term] +id: OBI:0002957 +name: reverse phase protein array profiling assay +def: "A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications." [] +synonym: "reverse phase lysate array profiling assay" EXACT [] +synonym: "RPLA assay" EXACT [] +synonym: "RPPA assay" EXACT [] +is_a: OBI:0002953 ! protein state assay + +[Term] +id: OBI:0002958 +name: SWATH-MS protein profiling assay +def: "A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides." [] +synonym: "sequential window acquisition of all theoretical mass spectra protein profiling assay" EXACT [] +is_a: OBI:0000615 ! protein expression profiling assay + +[Term] +id: OBI:0002959 +name: tandem mass tag mass spectrometry +def: "A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins." [] +is_a: OBI:0000470 ! mass spectrometry assay + +[Term] +id: OBI:0002960 +name: fluorescence imaging-based reporter gene assay +def: "A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression." [] +is_a: OBI:0001501 ! fluorescence detection assay +is_a: OBI:0002082 ! reporter gene assay + +[Term] +id: OBI:0002961 +name: global chromatin profiling by mass spectrometry assay +def: "A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin." [] +synonym: "GCP" EXACT [] +synonym: "global chromatin epigenetic profiling" EXACT [] +synonym: "global chromatin profiling" EXACT [] +is_a: OBI:0002020 ! epigenetic modification assay + +[Term] +id: OBI:0002962 +name: kinase inhibitor assay +def: "A type of assay that identifies compounds that inhibit the activity of kinases." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0002963 +name: KINOMEscan assay +def: "A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions." [] +is_a: OBI:0002962 ! kinase inhibitor assay + +[Term] +id: OBI:0002964 +name: KiNativ assay +def: "A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP." [] +is_a: OBI:0002962 ! kinase inhibitor assay + +[Term] +id: OBI:0002965 +name: landmark transcript profiling assay +def: "A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence." [] +synonym: "L1000 mRNA profiling assay" EXACT [] +is_a: OBI:0000424 ! transcription profiling assay + +[Term] +id: OBI:0002966 +name: microenvironment microarray assay +def: "A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity." [] +synonym: "MEMA assay" EXACT [] +is_a: OBI:0001977 ! cytometry assay + +[Term] +id: OBI:0002967 +name: microwestern meso-scale quantitative western blot assay +def: "A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose." [] +is_a: OBI:0000854 ! western blot assay + +[Term] +id: OBI:0002968 +name: positive/negative ion switching metabolite profiling assay +def: "A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples." [] +synonym: "positive/negative ion switching metabolomic assay" EXACT [] +is_a: OBI:0000366 ! metabolite profiling assay + +[Term] +id: OBI:0002969 +name: cyclic immunoflouroescence assay +def: "A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation." [] +is_a: OBI:0002119 ! microscopy assay + +[Term] +id: OBI:0002970 +name: multiplex bead-based protein state immunoassay +def: "A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states." [] +is_a: OBI:0002953 ! protein state assay + [Term] id: OBI:0002971 name: endotracheal tube specimen @@ -19814,7 +20036,7 @@ is_a: OBI:0002904 ! adult arthropod specimen collection process [Term] id: OBI:0003005 -name: device for resting of adult arthropods for collection +name: device for collection of resting adult arthropods 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 @@ -19951,6 +20173,332 @@ 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:0003029 +name: barcode target locus role +def: "An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR." [] +is_a: OBI:0000067 ! evaluant role + +[Term] +id: OBI:0003030 +name: oligonucleotide primer set +def: "A processed material that consists of oligonucleotides that bear a primer role." [] +is_a: OBI:0000047 ! processed material + +[Term] +id: OBI:0003031 +name: fluorogenic PCR assay +def: "A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores." [] +synonym: "TaqMan" EXACT [] +is_a: OBI:0002692 ! polymerase chain reaction assay + +[Term] +id: OBI:0003032 +name: genotyping by PCR assay +def: "A genotyping assay that uses polymerase chain reaction." [] +is_a: OBI:0000435 ! genotyping assay +is_a: OBI:0002692 ! polymerase chain reaction assay + +[Term] +id: OBI:0003033 +name: cleavage under targets and release using nuclease assay +def: "A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing." [] +synonym: "CUT&RUN assay" EXACT [] +is_a: OBI:0000626 ! DNA sequencing assay + +[Term] +id: OBI:0003034 +name: cleavage under targets and tagmentation +def: "A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing." [] +synonym: "CUT&Tag assay" EXACT [] +is_a: OBI:0000626 ! DNA sequencing assay + +[Term] +id: OBI:0003035 +name: coma severity assay +def: "A physical examination of individual that has the objective to determine the severity of coma in a patient." [] +is_a: OBI:0002441 ! physical examination of individual + +[Term] +id: OBI:0003036 +name: Plasmodium gametocyte detection assay +def: "An assay that detects Plasmodium gametocytes in a specimen." [] +is_a: OBI:0003038 ! parasite detection assay + +[Term] +id: OBI:0003037 +name: malaria rapid diagnosis assay +def: "An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood." [] +synonym: "malaria rapid diagnosis test" EXACT [] +is_a: OBI:0003038 ! parasite detection assay +is_a: OBI:0003040 ! blood assay + +[Term] +id: OBI:0003038 +name: parasite detection assay +def: "An assay that detects parasite in a specimen." [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003039 +name: feces microbiology assay +def: "An assay that detects microorganisms in a feces specimen." [] +synonym: "stool test for microorganisms" EXACT [] +is_a: OBI:0001624 ! organism identification assay + +[Term] +id: OBI:0003040 +name: blood assay +def: "An assay that has a blood specimen as evaulant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003041 +name: falcivax rapid diagnostic test +def: "A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood." [] +is_a: OBI:0003038 ! parasite detection assay +is_a: OBI:0003040 ! blood assay + +[Term] +id: OBI:0003042 +name: optimal-IT rapid diagnostic test +def: "A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites." [] +is_a: OBI:0003038 ! parasite detection assay +is_a: OBI:0003040 ! blood assay + +[Term] +id: OBI:0003043 +name: urine assay +def: "An assay that has a urine specimen as evaluant." [] +is_a: OBI:0000070 ! assay + +[Term] +id: OBI:0003044 +name: parasite species identification by PCR assay +def: "An organism identification assay that identifies the species of parasites by PCR." [] +is_a: OBI:0003045 ! parasite detection by PCR assay + +[Term] +id: OBI:0003045 +name: parasite detection by PCR assay +def: "An assay that detects parasite in a specimen using PCR." [] +is_a: OBI:0002692 ! polymerase chain reaction assay +is_a: OBI:0003038 ! parasite detection assay + +[Term] +id: OBI:0003046 +name: free-standing window trap +def: "An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die." [] +is_a: OBI:0002920 ! arthropod trap + +[Term] +id: OBI:0003048 +name: BG-lure scent dispenser +def: "A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin." [] +synonym: "BG-lure" EXACT [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0003049 +name: hand-held sweep net +def: "A device that consists of a network of mesh and is designed to capture adult arthropods." [] +is_a: OBI:0000968 ! device + +[Term] +id: OBI:0003050 +name: Centers for Disease Control and Prevention gravid trap +def: "A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan." [] +synonym: "CDC gravid trap" EXACT [] +is_a: OBI:0002929 ! gravid trap + +[Term] +id: OBI:0003051 +name: egg specimen collection process +def: "An arthropod specimen collection process in which the arthropods are in the embryo stage." [] +synonym: "collection of eggs" EXACT [] +is_a: OBI:0002907 ! aquatic arthropod specimen collection process + +[Term] +id: OBI:0003052 +name: larval specimen collection process +def: "An arthropod specimen collection process in which the arthropods are in the larval stage." [] +synonym: "collection of larvae" EXACT [] +is_a: OBI:0002907 ! aquatic arthropod specimen collection process + +[Term] +id: OBI:0003053 +name: pupal specimen collection process +def: "An arthropod specimen collection process in which the arthropods are in the pupal stage." [] +synonym: "collection of pupae" EXACT [] +is_a: OBI:0002907 ! aquatic arthropod specimen collection process + +[Term] +id: OBI:0003054 +name: blood specimen in vacutainer +def: "A blood specimen that is located in a vacutainer." [] +synonym: "Vacutainer sample" EXACT [] +is_a: OBI:2000009 ! bodily fluid specimen + +[Term] +id: OBI:0003055 +name: blood specimen on filter paper +def: "A blood specimen that is located on a filter paper." [] +synonym: "Filter paper sample" EXACT [] +is_a: OBI:2000009 ! bodily fluid specimen + +[Term] +id: OBI:0003056 +name: proportion mapped reads +def: "A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads." [] +is_a: OBI:0000973 ! sequence data + +[Term] +id: OBI:0003057 +name: antibiotic administration process +def: "Administering substance in vivo where an antibiotic substance is administered to a living organism." [] +is_a: OBI:0600007 ! administering substance in vivo + +[Term] +id: OBI:0003063 +name: insecticide resistance datum +def: "A data item that is about resistance to an insecticide." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003064 +name: organism identification datum +def: "A data item that is the specified output of an organism identification assay." [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003066 +name: easting coordinate measurement datum +def: "A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection." [] +is_a: IAO:0000401 ! one dimensional cartesian spatial coordinate datum + +[Term] +id: OBI:0003067 +name: northing coordinate measurement datum +def: "A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection." [] +is_a: IAO:0000401 ! one dimensional cartesian spatial coordinate datum + +[Term] +id: OBI:0003068 +name: clinical study center +def: "Organization that undertakes a clinical study at some point in time." [] +is_a: OBI:0000245 ! organization + +[Term] +id: OBI:0003069 +name: sequencing protocol +def: "A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial." [] +is_a: OBI:0000272 ! protocol + +[Term] +id: OBI:0003070 +name: specimen collection protocol +def: "A protocol that specifies processes to fulfill a specimen collection objective." [] +is_a: OBI:0000272 ! protocol + +[Term] +id: OBI:0003071 +name: participant identifier +def: "A symbol that denotes a participant under investigation." [] +is_a: IAO:0000028 ! symbol + +[Term] +id: OBI:0003072 +name: axillary temperature measurement datum +def: "A temperature measurement datum that is about an axilla." [] +is_a: OBI:0003079 ! temperature measurement datum + +[Term] +id: OBI:0003073 +name: organismal body temperature measurement datum +def: "A temperature measurement datum that is about an organism." [] +is_a: OBI:0003079 ! temperature measurement datum + +[Term] +id: OBI:0003074 +name: common name of organism +def: "A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized." [] +is_a: IAO:0000300 ! textual entity + +[Term] +id: OBI:0003075 +name: age since birth at time of enrollment +def: "An age since birth measurement datum at the time of subject enrollment." [] +is_a: OBI:0001169 ! age since birth measurement datum + +[Term] +id: OBI:0003076 +name: age since birth at time of visit +def: "An age since birth measurement datum at the time of a clinical visit." [] +is_a: OBI:0001169 ! age since birth measurement datum + +[Term] +id: OBI:0003077 +name: entomological data item +def: "A data item that is about a collection of insects." [] +synonym: "entomological measurement datum" EXACT [] +is_a: IAO:0000027 ! data item + +[Term] +id: OBI:0003079 +name: temperature measurement datum +def: "A scalar measurement datum that is the result of measuring temperature." [] +is_a: IAO:0000032 ! scalar measurement datum + +[Term] +id: OBI:0003080 +name: organismal body temperature measurement assay +def: "An assay that detects body temperature of an organism." [] +is_a: OBI:0002140 ! temperature measurement assay + +[Term] +id: OBI:0003081 +name: extraction date +def: "A time measurement datum that specifies when some material was extracted from an input material." [] +is_a: IAO:0000416 ! time measurement datum + +[Term] +id: OBI:0003082 +name: extraction duration time +def: "A time measurement datum that is the result of measuring the duration of an extraction process." [] +is_a: IAO:0000416 ! time measurement datum + +[Term] +id: OBI:0003083 +name: specimen collection time post disease onset +def: "A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host." [] +is_a: OBI:0001619 ! specimen collection time measurement datum + +[Term] +id: OBI:0003084 +name: specimen collection time post infection +def: "A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts." [] +is_a: OBI:0001619 ! specimen collection time measurement datum + +[Term] +id: OBI:0003085 +name: laboratory postal address +def: "A postal address used as a directive to deliver something to a laboratory." [] +synonym: "laboratory address" EXACT [] +is_a: IAO:0000422 ! postal address + +[Term] +id: OBI:0003086 +name: laboratory-based population +def: "A population where the collection of individuals is located and maintained in a laboratory, research, or production facility." [] +is_a: OBI:0000181 ! population + +[Term] +id: OBI:0003114 +name: Illumina MiniSeq +def: "A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run." [] +synonym: "MiniSeq" EXACT [] +is_a: OBI:0400103 ! DNA sequencer + [Term] id: OBI:0005246 name: injection function @@ -20033,7 +20581,8 @@ is_obsolete: true id: OBI:0100056 name: obsolete_immortal cell line culture def: "A cell line that is expected to be capable of indefinite propagation in an vitro culture." [] -synonym: "immortal cell line sample|permanent cell line" EXACT [] +synonym: "immortal cell line sample" EXACT [] +synonym: "permanent cell line" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: CLO:0009828 @@ -21320,8 +21869,8 @@ is_a: OBI:0500000 ! study design id: OBI:0302714 name: obsolete_collection (of entities of organismal origin) def: "a collection is a bfo:aggregate object, that is a set of material object of the same kind" [] -synonym: " ensemble" EXACT [] -synonym: " group" EXACT [] +synonym: "ensemble" EXACT [] +synonym: "group" EXACT [] synonym: "set" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true @@ -21364,6 +21913,7 @@ name: comet assay def: "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" [] synonym: "SCGE assay" EXACT [] synonym: "single cell gel electrophoresis assay" EXACT [] +is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:0001977 ! cytometry assay [Term] @@ -21563,7 +22113,7 @@ is_a: OBI:0600015 ! group assignment [Term] id: OBI:0302901 name: obsolete_activation -def: "a process by which a material entity status is modified and conferred a capability of reacting\n(this sounds like a circular definition , hugh!)" [] +def: "a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!)" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true @@ -23756,6 +24306,7 @@ name: MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR def: "A T cell epitope qualitative binding assay that uses an MHC multimer staining assay." [] synonym: "qualitative binding|multimer/tetramer" EXACT [] is_a: OBI:0001317 ! flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex +is_a: OBI:0001501 ! fluorescence detection assay [Term] id: OBI:1110180 @@ -24734,7 +25285,7 @@ is_a: OBI:2100034 ! prostate-specific antigen assay 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 +is_a: OBI:0003043 ! urine assay [Term] id: OBI:2100122 @@ -24830,24 +25381,28 @@ is_a: OBI:2100002 ! sodium(1+) assay 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:0003043 ! urine assay 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:0003043 ! urine assay 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:0003043 ! urine assay 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:0003043 ! urine assay is_a: OBI:2100039 ! osmolality assay [Term] @@ -24872,12 +25427,14 @@ is_a: OBI:2100040 ! methemoglobin assay 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:0003043 ! urine assay 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:0003043 ! urine assay is_a: OBI:2100004 ! potassium(1+) assay [Term] @@ -25242,6 +25799,7 @@ is_a: OBI:0000443 ! analyte assay id: OBI:2100205 name: urine protein assay def: "An analyte assay that measures the abundance of protein in urine" [] +is_a: OBI:0003043 ! urine assay is_a: OBI:2100023 ! protein assay [Term] @@ -25563,6 +26121,7 @@ is_a: OBI:2100045 ! tobramycin assay 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:0003043 ! urine assay is_a: OBI:2100003 ! creatinine assay [Term] @@ -25587,6 +26146,7 @@ is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay 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:0003043 ! urine assay is_a: OBI:2100023 ! protein assay [Term] @@ -25799,6 +26359,7 @@ is_a: OBI:2100004 ! potassium(1+) assay id: OBI:2100297 name: urine sodium assay def: "An analyte assay that measures the abundance of sodium in urine" [] +is_a: OBI:0003043 ! urine assay is_a: OBI:2100002 ! sodium(1+) assay [Term] @@ -26200,6 +26761,7 @@ is_a: OBI:0003022 ! neutrophil assay 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:0003043 ! urine assay is_a: OBI:2100003 ! creatinine assay [Term] @@ -26431,6 +26993,12 @@ 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:2100402 +name: pooled clone sequencing assay +def: "A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced." [] +is_a: OBI:0000626 ! DNA sequencing assay + [Term] id: OBI:9999994 name: chromium release assay @@ -26491,6 +27059,18 @@ 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: OPL:0000232 +name: parasite organism +def: "An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class." [] +is_a: OBI:0100026 ! organism + +[Term] +id: OPL:0000267 +name: Plasmodium gametocyte +def: "A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes" [] +is_a: NCBITaxon:5820 ! Plasmodium + [Term] id: ObsoleteClass name: Obsolete Class diff --git a/views/obi_core.owl b/views/obi_core.owl index 83c7cc12..cd8dd913 100644 --- a/views/obi_core.owl +++ b/views/obi_core.owl @@ -7,12 +7,11 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -59,8 +58,8 @@ Mervi Heiskanen Monnie McGee Norman Morrison - Philip Lord Philippe Rocca-Serra + Phillip Lord Pierre Grenon Richard Bruskiewich Richard Scheuermann @@ -79,7 +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. - 2021-04-06 + 2021-08-18 @@ -381,7 +380,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime + https://oborel.github.io/obo-relations/temporal-semantics/ @@ -392,12 +391,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - -