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Single-cell BCR/TCR assays #1726

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Sep 14, 2023
Merged

Single-cell BCR/TCR assays #1726

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6146082
Add single-cell BCR and TCR
sebastianduesing Aug 31, 2023
ec76a3b
Adds bulk BCR/TCR synonym
sebastianduesing Aug 31, 2023
18625ee
Merge branch 'master' into ntr_yale_08-31-23
jamesaoverton Sep 14, 2023
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98 changes: 98 additions & 0 deletions src/ontology/modules/assays.owl
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Expand Up @@ -19680,6 +19680,7 @@
<obo:IAO_0000115>A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample.</obo:IAO_0000115>
<obo:IAO_0000117>Rebecca Jackson</obo:IAO_0000117>
<obo:IAO_0000118>TCR repertoire sequencing assay</obo:IAO_0000118>
<obo:IAO_0000118>bulk TCR assay</obo:IAO_0000118>
<obo:IAO_0000119>doi:10.1186/s12896-017-0379-9</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1307</obo:IAO_0000233>
<rdfs:label>T cell receptor repertoire sequencing assay</rdfs:label>
Expand All @@ -19695,6 +19696,7 @@
<obo:IAO_0000117>Rebecca Jackson</obo:IAO_0000117>
<obo:IAO_0000118>Antibody repertoire sequencing assay</obo:IAO_0000118>
<obo:IAO_0000118>BCR repertoire sequencing assay</obo:IAO_0000118>
<obo:IAO_0000118>bulk BCR assay</obo:IAO_0000118>
<obo:IAO_0000119>doi:10.1186/s12896-017-0379-9</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1307</obo:IAO_0000233>
<rdfs:label>B cell receptor repertoire sequencing assay</rdfs:label>
Expand Down Expand Up @@ -26422,6 +26424,102 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003598 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003598">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0002991"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000067"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001010"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001010"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111>single cell B cell receptor repertoire sequencing assay</obo:IAO_0000111>
<obo:IAO_0000115>A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin.</obo:IAO_0000115>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>single-cell BCR assay</obo:IAO_0000118>
<rdfs:label>single cell B cell receptor repertoire sequencing assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003599 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003599">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0002990"/>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000055"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000067"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000081"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001010"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001010"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000087"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000067"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000111>single cell T cell receptor repertoire sequencing assay</obo:IAO_0000111>
<obo:IAO_0000115>A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin.</obo:IAO_0000115>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>single-cell TCR assay</obo:IAO_0000118>
<rdfs:label>single cell T cell receptor repertoire sequencing assay</rdfs:label>
</owl:Class>



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

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003601">
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6 changes: 4 additions & 2 deletions src/ontology/templates/assays.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -420,8 +420,8 @@ OBI:0002984 capture Hi-C assay cHi-C A Hi-C assay in which a selection step is
OBI:0002985 magnetic resonance imaging assay MRI An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging Rebecca Jackson|Alexander D. Bartnik, ORCID:0000-0001-9676-7377|Lucas M. Serra, ORCID:0000-0002-2104-0568|Alexander D. Diehl, ORCID:0000-0001-9990-8331|Mackenzie T. Smith, ORCID:0000-0002-9821-4132|William D. Duncan, ORCID:0000-0001-9625-1899|Lauren M. Wishnie, ORCID:0000-0002-7245-3450 https://github.com/obi-ontology/obi/issues/1290 subclass imaging assay NMR instrument ('has role' some 'magnetic resonance imaging evaluant role') (realizes some (concretizes some 'magnetic resonance pulse sequence protocol'))
OBI:0002986 computed tomography imaging assay CT scan|CAT scan|computed tomography scan 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. url:https://www.mayoclinic.org/tests-procedures/ct-scan/about/pac-20393675 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1290 subclass imaging assay computed tomography scanner
OBI:0002987 positron emission tomography imaging assay PET scan|positron emission tomography scan An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. url:https://en.wikipedia.org/wiki/Positron_emission_tomography Rebecca Jackson https://github.com/obi-ontology/obi/issues/1290 subclass imaging assay positron emission tomography scanner
OBI:0002990 T cell receptor repertoire sequencing assay TCR repertoire sequencing assay A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. doi:10.1186/s12896-017-0379-9 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1307 subclass sequencing assay
OBI:0002991 B cell receptor repertoire sequencing assay BCR repertoire sequencing assay|Antibody repertoire sequencing assay A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. doi:10.1186/s12896-017-0379-9 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1307 subclass sequencing assay
OBI:0002990 T cell receptor repertoire sequencing assay TCR repertoire sequencing assay|bulk TCR assay A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. doi:10.1186/s12896-017-0379-9 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1307 subclass sequencing assay
OBI:0002991 B cell receptor repertoire sequencing assay BCR repertoire sequencing assay|Antibody repertoire sequencing assay|bulk BCR assay A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. doi:10.1186/s12896-017-0379-9 Rebecca Jackson https://github.com/obi-ontology/obi/issues/1307 subclass sequencing assay
OBI:0003009 ferritin assay An assay that measures ferritin OBI James A. Overton, ORCID:0000-0001-5139-5557 equivalent assay ferritin complex
OBI:0003010 fibrinogen assay An assay that measures fibrinogen OBI James A. Overton, ORCID:0000-0001-5139-5558 equivalent assay fibrinogen complex
OBI:0003011 iron assay An analyte assay that measures the abundance of iron OBI James A. Overton, ORCID:0000-0001-5139-5559 equivalent analyte assay iron cation
Expand Down Expand Up @@ -650,7 +650,9 @@ OBI:0003583 cell viability assay A cytometry assay which measures the number
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: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:0003598 single cell B cell receptor repertoire sequencing assay single cell B cell receptor repertoire sequencing assay single-cell BCR assay A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin. Sebastian Duesing|Randi Vita subclass B cell receptor repertoire sequencing assay nucleic acid extract
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:0003599 single cell T cell receptor repertoire sequencing assay single cell T cell receptor repertoire sequencing assay single-cell TCR assay A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin. Sebastian Duesing|Randi Vita subclass T cell receptor repertoire sequencing assay nucleic acid extract
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')
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