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Merge pull request #234 from obophenotype/PV-like
Moved CL PV-like to PCL
2 parents b62a59c + 9364e5b commit 390e0c5

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‎src/ontology/bdso-edit.owl‎

Lines changed: 86 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -9,32 +9,34 @@ Prefix(dcterms:=<http://purl.org/dc/terms/>)
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Ontology(<http://purl.obolibrary.org/obo/PCL.owl>
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Import(<http://purl.obolibrary.org/obo/helper.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/cl_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/ensmusg_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/simple_marmoset_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/simple_human_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/ncbitaxon_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/pato_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/ro_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/simple_human_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/simple_marmoset_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/imports/uberon_import.owl>)
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Import(<http://purl.obolibrary.org/obo/bdscratch/patterns/definitions.owl>)
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Import(<http://purl.obolibrary.org/obo/helper.owl>)
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Import(<http://purl.obolibrary.org/obo/components/all_templates.owl>)
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# Annotation(dce:description "None")
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Annotation(dce:title "Brain Data Standards Cell Ontology")
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Annotation(dcterms:license <http://creativecommons.org/licenses/by/4.0/>)
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Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000099>))
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Declaration(Class(<http://purl.obolibrary.org/obo/CL_4023119>))
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Declaration(Class(<http://purl.obolibrary.org/obo/GO_0061534>))
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Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0070002>))
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Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0070007>))
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Declaration(Class(<http://purl.obolibrary.org/obo/PCL_0010001>))
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Declaration(Class(<http://purl.obolibrary.org/obo/PCL_0010002>))
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Declaration(Class(<http://purl.obolibrary.org/obo/PCL_1000002>))
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Declaration(Class(<http://purl.obolibrary.org/obo/PCL_1000004>))
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Declaration(Class(<http://purl.obolibrary.org/obo/PR_P60041>))
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Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000956>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002100>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002215>))
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Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002292>))
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Declaration(AnnotationProperty(dce:description))
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Declaration(AnnotationProperty(dce:title))
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Declaration(AnnotationProperty(dcterms:license))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010051>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010052>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010053>))
@@ -46,67 +48,115 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010058>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010059>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010060>))
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Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010061>))
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############################
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# Object Properties
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############################
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002100> (has soma location)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002100> "has soma location")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002215> (capable of)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002215> "capable of")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002292> (expresses)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002292> "expresses")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0015001> (has exemplar data)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015001> "has exemplar data")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0015002> (exemplar data of)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015002> "exemplar data of")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0015003> (subcluster of)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015003> "subcluster of")
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Declaration(AnnotationProperty(dce:contributor))
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Declaration(AnnotationProperty(dce:description))
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Declaration(AnnotationProperty(dce:title))
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Declaration(AnnotationProperty(dcterms:license))
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############################
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# Annotation Properties
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############################
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# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000028> (symbol)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000028> "symbol")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010051> (cell_type_rank)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010051> "cell_type_rank")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010052> (cell_types_count)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010052> "cell_types_count")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010053> (cell_subclasses_count)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010053> "cell_subclasses_count")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010054> (cell_classes_count)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010054> "cell_classes_count")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010055> (has_age)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010055> "has_age")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010056> (has_sex)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010056> "has_sex")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010057> (has_brain_region)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010057> "has_brain_region")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010058> (has nsforest marker)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010058> "has nsforest marker")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010059> (cluster id)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010059> "cluster id")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010060> (cell_count)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010060> "cell_count")
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# Annotation Property: <http://purl.obolibrary.org/obo/PCL_0010061> (nuclei_count)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_0010061> "nuclei_count")
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############################
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# Object Properties
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############################
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002100> (has soma location)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002100> "has soma location")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002215> (capable of)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002215> "capable of")
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# Object Property: <http://purl.obolibrary.org/obo/RO_0002292> (expresses)
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002292> "expresses")
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############################
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# Classes
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############################
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# Class: <http://purl.obolibrary.org/obo/CL_4023119> (basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus))
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AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:33184512") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/CL_4023119> "A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology.")
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AnnotationAssertion(dce:contributor <http://purl.obolibrary.org/obo/CL_4023119> <http://orcid.org/0000-0001-7258-9596>)
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_4023119> "basket L2/3 PV-like SST (Mus)")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_4023119> "basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
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SubClassOf(<http://purl.obolibrary.org/obo/CL_4023119> <http://purl.obolibrary.org/obo/PCL_1000002>)
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SubClassOf(<http://purl.obolibrary.org/obo/CL_4023119> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/PATO_0070002>))
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# Class: <http://purl.obolibrary.org/obo/PCL_1000002> (L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus))
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AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:33184512") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PCL_1000002> "A sst GABAergic cortical interneuron transcriptomically between the sst and the pvalb families with a soma found in L2/3. Some L2/3 PV-like sst cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like sst cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like sst cells have high maximum firing rate variability, with many classified as belonging to the pvalb subclass on the basis of electrophysiology.")
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AnnotationAssertion(dce:contributor <http://purl.obolibrary.org/obo/PCL_1000002> <http://orcid.org/0000-0001-7258-9596>)
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/PCL_1000002> "L2/3 PV-like SST Mus")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_1000002> "L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
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SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> <http://purl.obolibrary.org/obo/CL_0000099>)
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SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002100> <http://purl.obolibrary.org/obo/UBERON_0000956>))
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SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002100> <http://purl.obolibrary.org/obo/UBERON_8440000>))
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SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002162> <http://purl.obolibrary.org/obo/NCBITaxon_10090>))
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SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002215> <http://purl.obolibrary.org/obo/GO_0061534>))
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SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002292> <http://purl.obolibrary.org/obo/PR_P60041>))
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# Class: <http://purl.obolibrary.org/obo/PCL_1000004> (Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus))
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AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:33184512") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PCL_1000004> "A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology.")
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AnnotationAssertion(dce:contributor <http://purl.obolibrary.org/obo/PCL_1000004> <http://orcid.org/0000-0001-7258-9596>)
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AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/PCL_1000004> "Martinotti L2/3 PV-like SST (Mus)")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_1000004> "Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
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SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000004> <http://purl.obolibrary.org/obo/PCL_1000002>)
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SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000004> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/PATO_0070007>))
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000028> "symbol")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015001> "has exemplar data")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015002> "exemplar data of")
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AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015003> "subcluster of")
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)

‎src/patterns/data/default/CCN202002013_class_curation.tsv‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@ http://purl.obolibrary.org/obo/PCL_0011037 Sst Crhr2_2 ensembl:ENSMUSG000000
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http://purl.obolibrary.org/obo/PCL_0011038 Sst Hpse CL:4023031 PMID:34616066 ensembl:ENSMUSG00000004366|ensembl:ENSMUSG00000074852 PMID:34616062
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http://purl.obolibrary.org/obo/PCL_0011039 Sst Calb2 ensembl:ENSMUSG00000004366|ensembl:ENSMUSG00000003657 PMID:34616062
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http://purl.obolibrary.org/obo/PCL_0011040 Sst Pappa ensembl:ENSMUSG00000004366|ensembl:ENSMUSG00000028370 PMID:34616062
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http://purl.obolibrary.org/obo/PCL_0011041 Sst Pvalb Calb2 CL:4023034 PMID:34616066 ensembl:ENSMUSG00000004366|ensembl:ENSMUSG00000028370 Low Pvalb expression PMID:34616062
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http://purl.obolibrary.org/obo/PCL_0011041 Sst Pvalb Calb2 PCL:1000002 PMID:34616066 ensembl:ENSMUSG00000004366|ensembl:ENSMUSG00000028370 Low Pvalb expression PMID:34616062
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http://purl.obolibrary.org/obo/PCL_0011042 Sst C1ql3_1 ensembl:ENSMUSG00000004366|ensembl:ENSMUSG00000049630 PMID:34616062 This class represents a cross-species homology grouping. Cross-species clustering based on transcriptomic similarity supports the assertion that this class represents a homology grouping.
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http://purl.obolibrary.org/obo/PCL_0011043 Sst C1ql3_2 ensembl:ENSMUSG00000004366|ensembl:ENSMUSG00000049630 PMID:34616062
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http://purl.obolibrary.org/obo/PCL_0011044 Sst Tac2 ensembl:ENSMUSG00000004366|ensembl:ENSMUSG00000025400 PMID:34616062

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