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Merge pull request #1720 from obi-ontology/hcc_misc_terms
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Adding new terms for HCC
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@jamesaoverton
jamesaoverton committed Sep 14, 2023
2 parents 6536068 + 86f54a0 commit 7415b33
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Showing 9 changed files with 340 additions and 17 deletions.
2 changes: 1 addition & 1 deletion src/ontology/OntoFox_inputs/OGMS_input.txt
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Expand Up @@ -12,7 +12,7 @@ http://purl.obolibrary.org/obo/OGMS_0000063
http://purl.obolibrary.org/obo/OGMS_0000090
http://purl.obolibrary.org/obo/OGMS_0000031 # disease
http://purl.obolibrary.org/obo/OGMS_0000073 # diagnosis

http://purl.obolibrary.org/obo/OGMS_0000123 # clinical data item

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/OGMS_0000015
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38 changes: 33 additions & 5 deletions src/ontology/OntoFox_outputs/OGMS_imports.owl
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Expand Up @@ -24,15 +24,20 @@

<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
<obo:IAO_0000111 xml:lang="en">editor preferred term</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)</obo:IAO_0000115>
<rdfs:label xml:lang="en">editor preferred term</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<obo:IAO_0000111>definition</obo:IAO_0000111>
<rdfs:label>definition</rdfs:label>
<obo:IAO_0000111 xml:lang="en">definition</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
<rdfs:label xml:lang="en">definition</rdfs:label>
</owl:AnnotationProperty>


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<!-- http://purl.obolibrary.org/obo/IAO_0000027 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000111 xml:lang="en">data item</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
<rdfs:label xml:lang="en">data item</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/IAO_0000030 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030"/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
<obo:IAO_0000111 xml:lang="en">information content entity</obo:IAO_0000111>
<obo:IAO_0000115 xml:lang="en">A generically dependent continuant that is about some thing.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
<rdfs:label xml:lang="en">information content entity</rdfs:label>
</owl:Class>



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<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
<rdfs:label>treatment</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OGMS_0000123 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000123">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000111 xml:lang="en">clinical data item</obo:IAO_0000111>
<obo:IAO_0000115>A data item that is about a patient and is the specified output of a health care process assay or diagnostic process</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
<rdfs:label xml:lang="en">clinical data item</rdfs:label>
</owl:Class>
</rdf:RDF>


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33 changes: 27 additions & 6 deletions src/ontology/OntoFox_outputs/Uberon_imports.owl
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166 changes: 166 additions & 0 deletions src/ontology/modules/assays.owl
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Expand Up @@ -26250,6 +26250,172 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003587 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003587">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100060"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>An assay that has cell culture as an input.</obo:IAO_0000115>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<rdfs:label>cell culture assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003589 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003589">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0002145"/>
<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_0100017"/>
</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_0100017"/>
<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>
<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_0000275"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0019814"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001637"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10376"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</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/GO_0019814"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0001637"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10376"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample.</obo:IAO_0000115>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>EBV</obo:IAO_0000118>
<rdfs:label>serum anti-Epstein-Barr virus antibody level assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003590 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003590">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0002154"/>
<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_0100017"/>
</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_0100017"/>
<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>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<obo:IAO_0000115>A CMV antibody assay that has serum as an input.</obo:IAO_0000115>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<obo:IAO_0000118>CMV</obo:IAO_0000118>
<rdfs:label>serum anti-cytomegalovirus antibody level assay</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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43 changes: 43 additions & 0 deletions src/ontology/modules/biobank-specimens.owl
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Expand Up @@ -3912,6 +3912,49 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003595 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003595">
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0600005"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000659"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0001826"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<obo:IAO_0000115>A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space.</obo:IAO_0000115>
<obo:IAO_0000117>Randi Vita</obo:IAO_0000117>
<obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
<rdfs:label>nasal lavage fluid</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0100051 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100051"/>
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4 changes: 2 additions & 2 deletions src/ontology/modules/physical-examination.owl
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Expand Up @@ -156,7 +156,7 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003501">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0002441"/>
<obo:IAO_0000115>A physical examination of an individual&apos;s ability to perform functional activities.</obo:IAO_0000115>
<obo:IAO_0000115>A physical examination of an organism&apos;s ability to perform functional activities.</obo:IAO_0000115>
<obo:IAO_0000117>Daniel Olson, ORCID: 0000-0002-8134-1207</obo:IAO_0000117>
<obo:IAO_0000119>Critical Path Institute</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1637</obo:IAO_0000233>
Expand Down Expand Up @@ -1172,7 +1172,7 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003536">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0002441"/>
<obo:IAO_0000115>A physical examination of an individual through visual assesment.</obo:IAO_0000115>
<obo:IAO_0000115>A physical examination of an organism through visual assesment.</obo:IAO_0000115>
<obo:IAO_0000117>Daniel Olson, ORCID: 0000-0002-8134-1207</obo:IAO_0000117>
<obo:IAO_0000119>Critical Path Institute</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1637</obo:IAO_0000233>
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