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Moving 'QCM measuring KD' to epitope-assays
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Moves one term from the assay template to the epitope-assay template
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@sebastianduesing
sebastianduesing committed Aug 31, 2023
1 parent 74e96ff commit f4cb666
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Showing 4 changed files with 36 additions and 17 deletions.
16 changes: 0 additions & 16 deletions src/ontology/modules/assays.owl
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<!-- http://purl.obolibrary.org/obo/OBI_0003602 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003602">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003601"/>
<obo:IAO_0000111>quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex</obo:IAO_0000111>
<obo:IAO_0000115>A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody.</obo:IAO_0000115>
<obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>QCM measuring KD</obo:IAO_0000118>
<obo:IAO_0000119>IEDB</obo:IAO_0000119>
<rdfs:label>quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0100016 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100016"/>
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35 changes: 35 additions & 0 deletions src/ontology/modules/epitope-assays.owl
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<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
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<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118"/>



<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
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<!-- http://purl.obolibrary.org/obo/OBI_0003601 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003601"/>



<!-- http://purl.obolibrary.org/obo/OBI_0003602 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003602">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003601"/>
<obo:IAO_0000111>quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex</obo:IAO_0000111>
<obo:IAO_0000115>A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody.</obo:IAO_0000115>
<obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>QCM measuring KD</obo:IAO_0000118>
<obo:IAO_0000119>IEDB</obo:IAO_0000119>
<obo:OBI_9991118>dissociation constant KD|quartz crystal microbalance|nM</obo:OBI_9991118>
<rdfs:label>quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0600031 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0600031"/>
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1 change: 0 additions & 1 deletion src/ontology/templates/assays.tsv
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Expand Up @@ -649,7 +649,6 @@ OBI:0003582 cell proliferation assay using carboxyfluorescein succinimidyl ester
OBI:0003583 cell viability assay A cytometry assay which measures the number of living cells in a population. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 equivalent cytometry assay viability
OBI:0003584 cell viability assay using Annexin V staining A cell viability assay that uses Annexin V staining to detect apoptotic cells. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1007 equivalent cell viability assay Annexin V staining
OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay
OBI:0003602 quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex QCM measuring KD A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. IEDB Randi Vita|Bjoern Peters|Sebastian Duesing subclass quartz crystal microbalance assay
OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus
OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information')
OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course
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1 change: 1 addition & 0 deletions src/ontology/templates/epitope-assays.tsv
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Expand Up @@ -499,6 +499,7 @@ OBI:0003485 detection of specific nucleic acids with complementary probes assay
OBI:0003486 intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells IL-25 release|ICS A flow cytometry assay that detects interleukin-25 production by T cells. IEDB IEDB equivalent flow cytometry assay ('interleukin-25 production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
OBI:0003487 ELISA measuring epitope specific interleukin-25 production by T cells IL-25 release|ELISA An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells. IEDB IEDB equivalent enzyme-linked immunosorbent assay ('interleukin-25 production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
OBI:0003488 cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells TNF release|bioassay A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells. IEDB IEDB equivalent reporter cell line analyte detection bioassay ('tumor necrosis factor superfamily cytokine production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
OBI:0003602 quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex quartz crystal microbalance measuring the dissociation constant [KD] of a B cell epitope:antibody complex QCM measuring KD dissociation constant KD|quartz crystal microbalance|nM A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody. IEDB Randi Vita|Bjoern Peters|Sebastian Duesing subclass quartz crystal microbalance assay
OBI:1110013 ELISPOT assay measuring epitope specific interleukin-2 production by T cells IL-2 release|ELISPOT An enzyme-linked immunospot assay that detects interleukin-2 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interleukin-2 production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
OBI:1110037 assay measuring binding of a T cell epitope:MHC:TCR complex T cell binding|any method A T cell epitope assay that measures the binding of T cell receptor to an epitope. IEDB IEDB equivalent assay binding datum MHC:epitope complex binding to TCR
OBI:1110059 ELISPOT assay measuring epitope specific interferon-gamma production by T cells IFNg release|ELISPOT An enzyme-linked immunospot assay that detects interferon-gamma production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('interferon-gamma production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
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