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Adding hypertension grade and QCM terms #1721

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Sep 14, 2023
Merged

Adding hypertension grade and QCM terms #1721

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c8adbd8
Adding hypertension grade and QCM terms
sebastianduesing Jul 28, 2023
74e96ff
Fixing error in 'QCM assay measuring...'
sebastianduesing Aug 31, 2023
f4cb666
Moving 'QCM measuring KD' to epitope-assays
sebastianduesing Aug 31, 2023
dd731fc
Adding logic to QCM measuring KD
sebastianduesing Sep 7, 2023
aa0fcd6
Merge branch 'master' into hcc_terms_07-28-23
jamesaoverton Sep 14, 2023
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25 changes: 24 additions & 1 deletion src/ontology/modules/assays.owl
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Expand Up @@ -22,6 +22,12 @@



<!-- 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"/>
Expand Down Expand Up @@ -26416,6 +26422,23 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003601 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003601">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
<obo:IAO_0000111>quartz crystal microbalance assay</obo:IAO_0000111>
<obo:IAO_0000115>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.</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</obo:IAO_0000118>
<obo:IAO_0000119>http://www.ncbi.nlm.nih.gov/pubmed/23504432</obo:IAO_0000119>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Quartz_crystal_microbalance</obo:IAO_0000119>
<rdfs:label>quartz crystal microbalance assay</rdfs:label>
</owl:Class>



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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100016"/>
Expand Down Expand Up @@ -53185,5 +53208,5 @@



<!-- Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->

63 changes: 63 additions & 0 deletions src/ontology/modules/epitope-assays.owl
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Expand Up @@ -22,6 +22,12 @@



<!-- 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"/>
Expand All @@ -40,6 +46,12 @@



<!-- 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"/>
Expand Down Expand Up @@ -22721,6 +22733,57 @@



<!-- 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"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001536"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001702"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/UO_0000065"/>
</owl:Restriction>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<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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20 changes: 20 additions & 0 deletions src/ontology/modules/value-specifications.owl
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Expand Up @@ -22,6 +22,12 @@



<!-- 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"/>
Expand Down Expand Up @@ -524,6 +530,20 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003600 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003600">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001930"/>
<obo:IAO_0000111>hypertension grade</obo:IAO_0000111>
<obo:IAO_0000115>A categorical value specification that indicates the severity of hypertension.</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>
<rdfs:label>hypertension grade</rdfs:label>
</owl:Class>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
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1 change: 1 addition & 0 deletions src/ontology/templates/assays.tsv
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Expand Up @@ -651,6 +651,7 @@ OBI:0003584 cell viability assay using Annexin V staining A cell viability as
OBI:0003587 cell culture assay An assay that has cell culture as an input. Sebastian Duesing|Randi Vita equivalent assay cultured cell population
OBI:0003589 serum anti-Epstein-Barr virus antibody level assay EBV An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample. Sebastian Duesing|Randi Vita equivalent antigen specific antibodies assay blood serum specimen ('immunoglobulin complex' and ('has disposition to bind' some 'Human gammaherpesvirus 4'))
OBI:0003590 serum anti-cytomegalovirus antibody level assay CMV A CMV antibody assay that has serum as an input. Sebastian Duesing|Randi Vita equivalent CMV antibody assay blood serum specimen
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: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 equilibrium dissociation constant (KD) immunoglobulin binding to epitope nanomolar
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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1 change: 1 addition & 0 deletions src/ontology/templates/value-specifications.tsv
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Expand Up @@ -171,3 +171,4 @@ OBI:0002366 60-70: symptomatic but in bed less than 50% of the day A Karnofsk
OBI:0002367 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. NCI BBRB, OBI Chris Stoeckert, Helena Ellis NCI BBRB Karnofsky score vaue specification
OBI:0002490 medication time value specification medication timepoint A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material OBI John Judkins VEuPathDB subclass scalar value specification
OBI:0002491 medication dose value specification medication dose A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment OBI John Judkins VEuPathDB subclass scalar value specification
OBI:0003600 hypertension grade hypertension grade A categorical value specification that indicates the severity of hypertension. Randi Vita|Bjoern Peters|Sebastian Duesing subclass categorical value specification
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