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Add gene and related entities from SO #179

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Add gene and related entities from SO #179

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ac1c7f4
First pass at gene
cmungall Sep 13, 2021
1fd7753
MSO alignment
cmungall Sep 13, 2021
3060e4b
gene template relation from PR
cmungall Sep 13, 2021
5c37088
Merge branch 'master' into gene
matentzn Nov 29, 2022
22c4560
Update cob-idranges.owl
matentzn Nov 29, 2022
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178 changes: 176 additions & 2 deletions src/ontology/cob-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/">
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-edit.owl">
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cob/cob-annotations.owl"/>
<dc:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</dc:description>
Expand Down Expand Up @@ -50,6 +51,12 @@



<!-- http://purl.org/dc/elements/1.1/creator -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>



<!-- http://purl.org/dc/elements/1.1/description -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
Expand All @@ -68,6 +75,14 @@



<!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym">
<rdfs:label xml:lang="en">has exact synonym</rdfs:label>
</owl:AnnotationProperty>



<!-- http://www.w3.org/2004/02/skos/core#exactMatch -->

<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#exactMatch"/>
Expand Down Expand Up @@ -278,6 +293,25 @@



<!-- http://purl.obolibrary.org/obo/COB_0000508 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000508">
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000509"/>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cjm</dc:creator>
<rdfs:label xml:lang="en">has gene template</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/COB_0000509 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000509">
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cjm</dc:creator>
<rdfs:label xml:lang="en">gene template of</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/COB_0000512 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/COB_0000512">
Expand Down Expand Up @@ -527,7 +561,7 @@
<!-- http://purl.obolibrary.org/obo/COB_0000015 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000073"/>
<rdfs:label xml:lang="en">protein</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -596,6 +630,10 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000006"/>
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000118"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000507"/>
</owl:disjointUnionOf>
<obo:IAO_0000115>A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome.</obo:IAO_0000115>
<rdfs:comment>&quot;Maximal functionally integrated unit&quot; is intended to express unity, which Barry considers synonymous with BFO &apos;object&apos;.</rdfs:comment>
<rdfs:comment>Includes virus - we will later have a class for cellular organisms.</rdfs:comment>
Expand Down Expand Up @@ -915,6 +953,12 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000073">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000508"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000501"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>gene product</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -1299,6 +1343,31 @@



<!-- http://purl.obolibrary.org/obo/COB_0000501 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000501">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000503"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000509"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000049"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000509"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000073"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A sequence of nucleic acids that is part of a genome and is the template for one or more RNA molecules, where those molecules are either gene products or can be translated into gene products.</obo:IAO_0000115>
<obo:IAO_0000116>Add a GCI axiom: (gene and &apos;part of&apos; some &apos;cellular organism&apos;) SubClassOf &apos;part of&apos; some DNA</obo:IAO_0000116>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cjm</dc:creator>
<rdfs:comment>Genes are part of DNA in all organisms except RNA viruses. The definition needs tuning for positive-sense RNA viruses such as SARS-CoV-2. The viruses have an RNA genome that is directly translated and then cleaved into distinct functional polyproteins.</rdfs:comment>
<rdfs:label xml:lang="en">gene</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/COB_0000502 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000502">
Expand Down Expand Up @@ -1340,6 +1409,111 @@



<!-- http://purl.obolibrary.org/obo/COB_0000503 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000503">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000504"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000072"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000049"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000504"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000072"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000049"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115>A molecular entity that is composed of nucleic acid bases connected in a continuous sequence in the 5&apos; to 3&apos; direction.</obo:IAO_0000115>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cjm</dc:creator>
<oboInOwl:hasExactSynonym>sequence of nucleic acids</oboInOwl:hasExactSynonym>
<rdfs:label xml:lang="en">nucleotide region</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/COB_0000504 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000504">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000503"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000506"/>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000072"/>
<owl:someValuesFrom>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000015"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000049"/>
</owl:unionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000503"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000506"/>
</owl:disjointUnionOf>
<obo:IAO_0000115>A nucleotide region or a polypeptide region.</obo:IAO_0000115>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cjm</dc:creator>
<rdfs:comment>sequence of nucleotides or amino acids</rdfs:comment>
<rdfs:label xml:lang="en">region of nucleic acid polymer or protein</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0000504"/>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#subClassOf"/>
<owl:annotatedTarget rdf:resource="http://purl.obolibrary.org/obo/COB_0000013"/>
<rdfs:comment>In MSO this is not part of a molecular entity</rdfs:comment>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/COB_0000506 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000506">
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0000504"/>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/COB_0000072"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/COB_0000015"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000504"/>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cjm</dc:creator>
<oboInOwl:hasExactSynonym>amino acid sequence</oboInOwl:hasExactSynonym>
<rdfs:label xml:lang="en">polypeptide region</rdfs:label>
<skos:exactMatch rdf:resource="http://purl.obolibrary.org/obo/MSO_0000839"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/COB_0000507 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0000507">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/COB_0000022"/>
<dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cjm</dc:creator>
<rdfs:label xml:lang="en">virus</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/COB_0001000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001000">
Expand Down
13 changes: 10 additions & 3 deletions src/ontology/cob-idranges.owl
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Expand Up @@ -30,14 +30,21 @@ AnnotationProperty: idsfor:

AnnotationProperty: allocatedto:

Datatype: idrange:1
Datatype: idrange:0

Annotations:
allocatedto: "COB Core Team"
allocatedto: "Rebecca Jackson"

EquivalentTo:
xsd:integer[>= 0 , <= 999]
xsd:integer[>= 0 , < 500]

Datatype: idrange:1

Annotations:
allocatedto: "Chris Mungall"

EquivalentTo:
xsd:integer[>= 500 , < 1000]

Datatype: idrange:2

Expand Down
10 changes: 9 additions & 1 deletion src/ontology/components/cob-to-external.tsv
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Expand Up @@ -34,7 +34,6 @@ COB:0000003 mass owl:equivalentClass PATO:0000125 mass . HumanCurated
COB:0000004 charge owl:equivalentClass PATO:0002193 electric . HumanCurated
COB:0000005 elementary charge rdfs:subClassOf owl:Thing owl:Thing Making ticket in PATO tracker HumanCurated
COB:0000006 material entity owl:equivalentClass BFO:0000040 material entity . HumanCurated
COB:0000006 material entity sssom:superClassOf SO:0000110 sequence_feature . HumanCurated
COB:0000006 material entity sssom:superClassOf SO:0001060 sequence_variant . HumanCurated
COB:0000006 material entity sssom:superClassOf SO:0001260 sequence_collection . HumanCurated
COB:0000007 subatomic particle owl:equivalentClass CHEBI:36342 subatomic particle . HumanCurated
Expand Down Expand Up @@ -136,3 +135,12 @@ COB:0000029 realized in owl:equivalentProperty BFO:0000054 realized in . HumanCu
COB:0000513 is about owl:equivalentProperty IAO:0000136 is about There is no inverse for 'is about' in IAO. HumanCurated
COB:0000123 agent role owl:equivalentClass SEPIO:0000048 agent role HumanCurated
COB:0000123 agent role sssom:superClassOf OBI:0000202 investigation agent role HumanCurated
COB:0000501 gene owl:equivalentClass SO:0000704 gene .
COB:0000501 gene owl:equivalentClass MSO:0000704 gene .
COB:0000503 nucleotide region owl:equivalentClass MSO:3100210 nucleotide region In MSO can be part of dsDNA molecule
COB:0000503 nucleotide region owl:subClassOf SO:0000001 region .
COB:0000504 region of nucleic acid polymer or protein owl:equivalentClass SO:0000001 region .
COB:0000504 region of nucleic acid polymer or protein owl:equivalentClass MSO:0000001 sequence molecular entity region MSO defines as two or more sequence units
COB:0000506 polypeptide region owl:equivalentClass SO:0000839 polypeptide region .
COB:0000506 polypeptide region owl:equivalentClass MSO:0000839 peptide region MSO defines as two or more sequence units
COB:0000507 virus owl:equivalentClass NCBITaxon:10239 Viruses .