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updated VO and OBI imports to fix PR_P0DTC4 with wrong IRI issue, #45
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@zhengj2007
zhengj2007 committed Feb 15, 2024
1 parent ffbf09f commit ba1c203
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2 changes: 2 additions & 0 deletions src/ontology/Ontofox input/OBI_imports_input.txt
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Expand Up @@ -45,6 +45,8 @@ http://purl.obolibrary.org/obo/OBI_0000406 #PCR product
http://purl.obolibrary.org/obo/CHEBI_4705 #double-stranded DNA
http://purl.obolibrary.org/obo/BFO_0000019 #quality
http://purl.obolibrary.org/obo/BFO_0000144 # process profile
http://purl.obolibrary.org/obo/OBI_0000725 #host role
http://purl.obolibrary.org/obo/OBI_0000070

http://purl.obolibrary.org/obo/OBI_0000415 # PCR, polymerase chain reaction
http://purl.obolibrary.org/obo/OBI_0000552 # RT-PCR, reverse transcribed polymerase chain reaction
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1 change: 1 addition & 0 deletions src/ontology/Ontofox input/VO_imports_input.txt
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Expand Up @@ -12,6 +12,7 @@ http://purl.obolibrary.org/obo/VO_0005242 # up-expressed as immune signature of

[Top level source term URIs and target direct superclass URIs]
http://purl.obolibrary.org/obo/VO_0000001 # vaccine
subClassOf http://purl.obolibrary.org/obo/OBI_0000047

[Source term retrieval setting]
includeAllIntermediates
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69 changes: 10 additions & 59 deletions src/ontology/cido-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -452,8 +452,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An
<oboInOwl:shorthand>part_of</oboInOwl:shorthand>
<rdfs:label xml:lang="en">is part of</rdfs:label>
<rdfs:label xml:lang="en">part of</rdfs:label>
<rdfs:label xml:lang="en">part_of</rdfs:label>
<rdfs:label>part_of</rdfs:label>
<rdfs:label xml:lang="en">part_of</rdfs:label>
<rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections"/>
<rdfs:seeAlso rdf:resource="http://ontologydesignpatterns.org/wiki/Submissions:PartOf"/>
<rdfs:seeAlso>http://www.obofoundry.org/ro/#OBO_REL:part_of</rdfs:seeAlso>
Expand Down Expand Up @@ -496,8 +496,8 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.
<oboInOwl:id>has_part</oboInOwl:id>
<oboInOwl:is_cyclic rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</oboInOwl:is_cyclic>
<oboInOwl:shorthand>has_part</oboInOwl:shorthand>
<rdfs:label xml:lang="en">has part</rdfs:label>
<rdfs:label>has part</rdfs:label>
<rdfs:label xml:lang="en">has part</rdfs:label>
<rdfs:label>has_part</rdfs:label>
</owl:ObjectProperty>

Expand Down Expand Up @@ -9768,36 +9768,6 @@ results from evaporation of droplets coughed or sneezed into the atmosphere or b

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CIDO_0000311">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000314"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/VO_0004989"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000307"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000308"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000309"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000312"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000310"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000117>Anthony Huffman, Oliver He</obo:IAO_0000117>
<obo:IAO_0000119>https://pubmed.ncbi.nlm.nih.gov/32753554/</obo:IAO_0000119>
<rdfs:label xml:lang="en">SLLIVNNATNVVIKV</rdfs:label>
Expand Down Expand Up @@ -38019,7 +37989,6 @@ This kit is used for in vitro qualitative detection of novel coronavirus (2019-n
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/vo.owl"/>
<oboInOwl:hasBroadSynonym>SARS-CoV-2</oboInOwl:hasBroadSynonym>
<oboInOwl:hasDbXref>GC_ID:1</oboInOwl:hasDbXref>
<oboInOwl:hasExactSynonym>Wuhan coronavirus</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>2019-nCoV</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>COVID-19</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>COVID-19 virus</oboInOwl:hasExactSynonym>
Expand All @@ -38030,6 +37999,7 @@ This kit is used for in vitro qualitative detection of novel coronavirus (2019-n
<oboInOwl:hasExactSynonym>SARS-CoV-2</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>SARS-CoV2</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>SARS2</oboInOwl:hasExactSynonym>
<oboInOwl:hasExactSynonym>Wuhan coronavirus</oboInOwl:hasExactSynonym>
<oboInOwl:hasOBONamespace>ncbi_taxonomy</oboInOwl:hasOBONamespace>
<oboInOwl:id>NCBITaxon:2697049</oboInOwl:id>
<rdfs:comment>The list of the marker variants is as follows (as of 3/6/2021):
Expand Down Expand Up @@ -39204,6 +39174,12 @@ Reference: https://www.gisaid.org/references/statements-clarifications/clade-and



<!-- http://purl.obolibrary.org/obo/OBI_0000070 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>



<!-- http://purl.obolibrary.org/obo/OBI_0000576 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000576"/>
Expand Down Expand Up @@ -62243,31 +62219,6 @@ Reference: https://www.gisaid.org/references/statements-clarifications/clade-and



<!-- http://purl.obolibrary.org/obo/VO_0004989 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/VO_0004989">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000410"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000445"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000410"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000446"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000410"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CIDO_0000447"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/VO_0005159 -->

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/VO_0005159">
Expand Down Expand Up @@ -62577,5 +62528,5 @@ Reference: https://www.gisaid.org/references/statements-clarifications/clade-and



<!-- 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 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->

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