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Merge cns interneuron interneuron term #2686

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merged 12 commits into from
Dec 18, 2024
Merged

Merge cns interneuron interneuron term #2686

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d407204
Merge CNS interneuron with interneuron
AvolaAmg Oct 21, 2024
43a63ec
merge CNS interneuron
AvolaAmg Oct 21, 2024
45571e7
Update cl-edit.owl
AvolaAmg Oct 21, 2024
5b7ca08
Merge branch 'master' into Merge-CNS-interneuron-interneuron-term
AvolaAmg Oct 28, 2024
6de601c
Update cl-edit.owl
AvolaAmg Oct 28, 2024
b05e222
Merge branch 'Merge-CNS-interneuron-interneuron-term' of https://gith…
AvolaAmg Oct 28, 2024
a519da2
Update cl-edit.owl
AvolaAmg Oct 28, 2024
2333d58
Fixing QC fail
AvolaAmg Oct 28, 2024
7cc1baa
Merge branch 'master' into Merge-CNS-interneuron-interneuron-term
Caroline-99 Dec 6, 2024
db4f84b
Merge branch 'master' into Merge-CNS-interneuron-interneuron-term
Caroline-99 Dec 16, 2024
0c02d7b
Merge branch 'master' into Merge-CNS-interneuron-interneuron-term
Caroline-99 Dec 17, 2024
30b3f33
Merge branch 'master' into Merge-CNS-interneuron-interneuron-term
Caroline-99 Dec 18, 2024
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18 changes: 6 additions & 12 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -449,7 +449,6 @@ Declaration(Class(obo:CL_0000398))
Declaration(Class(obo:CL_0000399))
Declaration(Class(obo:CL_0000400))
Declaration(Class(obo:CL_0000401))
Declaration(Class(obo:CL_0000402))
Declaration(Class(obo:CL_0000403))
Declaration(Class(obo:CL_0000404))
Declaration(Class(obo:CL_0000405))
Expand Down Expand Up @@ -4565,8 +4564,10 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "BTO:0003811")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "FMA:67313")
AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "WBbt:0005113")
AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000099 "CNS interneuron")
AnnotationAssertion(rdfs:label obo:CL_0000099 "interneuron")
SubClassOf(obo:CL_0000099 obo:CL_0000540)
SubClassOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017))

# Class: obo:CL_0000100 (motor neuron)

Expand Down Expand Up @@ -7034,13 +7035,6 @@ AnnotationAssertion(rdfs:comment obo:CL_0000401 "Obsoleted as plasmatocytes are
AnnotationAssertion(rdfs:label obo:CL_0000401 "obsolete macrophage (sensu Diptera)")
AnnotationAssertion(owl:deprecated obo:CL_0000401 "true"^^xsd:boolean)

# Class: obo:CL_0000402 (CNS interneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1016/B978-0-12-817424-1.00001-X") obo:IAO_0000115 obo:CL_0000402 "An interneuron that has its cell body in a central nervous system.")
AnnotationAssertion(rdfs:comment obo:CL_0000402 "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system.")
AnnotationAssertion(rdfs:label obo:CL_0000402 "CNS interneuron")
EquivalentClasses(obo:CL_0000402 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017)))

# Class: obo:CL_0000403 (obo:CL_0000403)

AnnotationAssertion(obo:IAO_0000231 obo:CL_0000403 obo:IAO_0000227)
Expand All @@ -7063,7 +7057,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0000405 "true"^^xsd:boolean)
# Class: obo:CL_0000406 (CNS short range interneuron)

AnnotationAssertion(rdfs:label obo:CL_0000406 "CNS short range interneuron")
SubClassOf(obo:CL_0000406 obo:CL_0000402)
SubClassOf(obo:CL_0000406 obo:CL_0000099)

# Class: obo:CL_0000407 (scolopidial ligament cell)

Expand Down Expand Up @@ -7091,7 +7085,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0000409 "true"^^xsd:boolean)
# Class: obo:CL_0000410 (CNS long range interneuron)

AnnotationAssertion(rdfs:label obo:CL_0000410 "CNS long range interneuron")
SubClassOf(obo:CL_0000410 obo:CL_0000402)
SubClassOf(obo:CL_0000410 obo:CL_0000099)

# Class: obo:CL_0000411 (Caenorhabditis hypodermal cell)

Expand Down Expand Up @@ -21366,7 +21360,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0004001 "cell")
AnnotationAssertion(oboInOwl:id obo:CL_0004001 "CL:0004001")
AnnotationAssertion(rdfs:comment obo:CL_0004001 "Local interneurons form the category of interneurons whose axon stays entirely within the gray matter region where the cell body resides (Swanson, 2003, p. 245; Bota and Swanson, 2007, Fig. 3).")
AnnotationAssertion(rdfs:label obo:CL_0004001 "local interneuron")
SubClassOf(obo:CL_0004001 obo:CL_0000402)
SubClassOf(obo:CL_0004001 obo:CL_0000099)
SubClassOf(obo:CL_0004001 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002020))

# Class: obo:CL_0004115 (retinal ganglion cell B)
Expand Down Expand Up @@ -22036,7 +22030,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CL:CVS") obo:IAO_0000115 obo:
AnnotationAssertion(rdfs:comment obo:CL_0005000 "Is_a interneuron, part_of UBERON:0002240.")
AnnotationAssertion(rdfs:label obo:CL_0005000 "spinal cord interneuron")
EquivalentClasses(obo:CL_0005000 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002240)))
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0005000 obo:CL_0000402)
SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0005000 obo:CL_0000099)

# Class: obo:CL_0005001 (iridoblast)

Expand Down
9 changes: 9 additions & 0 deletions src/ontology/components/hra_subset.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,12 @@



<!-- http://purl.obolibrary.org/obo/IAO_0100001 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>



<!-- http://purl.obolibrary.org/obo/RO_0002175 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002175"/>
Expand Down Expand Up @@ -553,8 +559,11 @@
<!-- http://purl.obolibrary.org/obo/CL_0000402 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0000402">
<obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/CL_0000099"/>
<obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_9606"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas"/>
<rdfs:comment>https://github.com/obophenotype/cell-ontology/pull/2686</rdfs:comment>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>


Expand Down
18 changes: 8 additions & 10 deletions src/ontology/components/mappings.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -645,6 +645,7 @@
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000099">
<oboInOwl:hasDbXref>FBbt:00005125</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>ZFA:0009051</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>ZFA:0009191</oboInOwl:hasDbXref>
</rdf:Description>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0000099"/>
Expand All @@ -658,6 +659,12 @@
<owl:annotatedTarget>ZFA:0009051</owl:annotatedTarget>
<sssom:mapping_justification rdf:resource="https://w3id.org/semapv/vocab/UnspecifiedMatching"/>
</owl:Axiom>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0000099"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<owl:annotatedTarget>ZFA:0009191</owl:annotatedTarget>
<sssom:mapping_justification rdf:resource="https://w3id.org/semapv/vocab/UnspecifiedMatching"/>
</owl:Axiom>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000100">
<oboInOwl:hasDbXref>FBbt:00005123</oboInOwl:hasDbXref>
<oboInOwl:hasDbXref>ZFA:0009052</oboInOwl:hasDbXref>
Expand Down Expand Up @@ -2006,15 +2013,6 @@
<owl:annotatedTarget>FBbt:00001687</owl:annotatedTarget>
<sssom:mapping_justification rdf:resource="https://w3id.org/semapv/vocab/ManualMappingCuration"/>
</owl:Axiom>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000402">
<oboInOwl:hasDbXref>ZFA:0009191</oboInOwl:hasDbXref>
</rdf:Description>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0000402"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<owl:annotatedTarget>ZFA:0009191</owl:annotatedTarget>
<sssom:mapping_justification rdf:resource="https://w3id.org/semapv/vocab/UnspecifiedMatching"/>
</owl:Axiom>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000404">
<oboInOwl:hasDbXref>ZFA:0009193</oboInOwl:hasDbXref>
</rdf:Description>
Expand Down Expand Up @@ -4563,5 +4561,5 @@



<!-- Generated by the OWL API (version 4.5.29) 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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