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Add L4 IT #233

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Add L4 IT #233

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228a363
Added L4 IT
shawntanzk Dec 16, 2021
f665798
Update bdso-edit.owl
shawntanzk Dec 16, 2021
5e3faf9
Merge branch 'pcl_migration' into L4-IT
shawntanzk Jan 11, 2022
aff0e05
Update mistake in IRI
shawntanzk Jan 11, 2022
3d2d4b9
Merge branch 'master' into L4-IT
shawntanzk Feb 16, 2022
9911966
Update bdso-edit.owl
shawntanzk Feb 17, 2022
7b05945
Update bdso-edit.owl
shawntanzk Feb 17, 2022
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44 changes: 27 additions & 17 deletions src/ontology/bdso-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,24 +12,26 @@ Ontology(<http://purl.obolibrary.org/obo/PCL.owl>
Import(<http://purl.obolibrary.org/obo/helper.owl>)
Import(<http://purl.obolibrary.org/obo/bdscratch/imports/simple_human_import.owl>)
Import(<http://purl.obolibrary.org/obo/bdscratch/imports/simple_marmoset_import.owl>)
Import(<http://purl.obolibrary.org/obo/pcl/imports/merged_import.owl>)
Import(<http://purl.obolibrary.org/obo/bdscratch/patterns/definitions.owl>)
Import(<http://purl.obolibrary.org/obo/components/all_templates.owl>)
Import(<http://purl.obolibrary.org/obo/pcl/imports/merged_import.owl>)
Annotation(dce:title "Brain Data Standards Cell Ontology")
Annotation(dcterms:license <http://creativecommons.org/licenses/by/4.0/>)

Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000099>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_4023119>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_4023040>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0061534>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0070002>))
Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0070007>))
Declaration(Class(<http://purl.obolibrary.org/obo/PCL_0010001>))
Declaration(Class(<http://purl.obolibrary.org/obo/PCL_0010002>))
Declaration(Class(<http://purl.obolibrary.org/obo/PCL_1000000>))
Declaration(Class(<http://purl.obolibrary.org/obo/PCL_1000002>))
Declaration(Class(<http://purl.obolibrary.org/obo/PCL_1000003>))
Declaration(Class(<http://purl.obolibrary.org/obo/PCL_1000004>))
Declaration(Class(<http://purl.obolibrary.org/obo/PR_P60041>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000956>))
Declaration(Class(<http://purl.obolibrary.org/obo/SO_0001260>))
Declaration(Class(<http://purl.obolibrary.org/obo/UBERON_0000956>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002100>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002215>))
Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0002292>))
Expand All @@ -46,14 +48,15 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010059>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010060>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/PCL_0010061>))
Declaration(AnnotationProperty(dce:contributor))
Declaration(AnnotationProperty(dce:creator))
Declaration(AnnotationProperty(dce:description))
Declaration(AnnotationProperty(dce:title))
Declaration(AnnotationProperty(dcterms:description))
Declaration(AnnotationProperty(dcterms:license))
Declaration(AnnotationProperty(dcterms:title))
Declaration(AnnotationProperty(dcterms:provenance))
Declaration(AnnotationProperty(dcterms:description))
Declaration(AnnotationProperty(dcterms:subject))
Declaration(AnnotationProperty(dcterms:relation))
Declaration(AnnotationProperty(dcterms:subject))
Declaration(AnnotationProperty(dcterms:title))
############################
# Annotation Properties
############################
Expand Down Expand Up @@ -129,18 +132,18 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015004> "has
# Classes
############################

# Class: <http://purl.obolibrary.org/obo/CL_4023119> (basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus))
# Class: <http://purl.obolibrary.org/obo/PCL_1000000> (L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex)

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.")
AnnotationAssertion(dce:contributor <http://purl.obolibrary.org/obo/CL_4023119> <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/CL_4023119> "basket L2/3 PV-like SST (Mus)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/CL_4023119> "basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
SubClassOf(<http://purl.obolibrary.org/obo/CL_4023119> <http://purl.obolibrary.org/obo/PCL_1000002>)
SubClassOf(<http://purl.obolibrary.org/obo/CL_4023119> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/PATO_0070002>))
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:33184512"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PCL_1000000> "An intratelencephalic-projecting glutamatergic neuron that is located in the boundary between L2/3 and L5 of the primary motor cortex. These cells have diverse morphologies with some pyramidal and some stellate cells.")
AnnotationAssertion(dcterms:creator <http://purl.obolibrary.org/obo/PCL_1000000> <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/PCL_1000000> "ILX:0770172")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:25525751") rdfs:comment <http://purl.obolibrary.org/obo/PCL_1000000> "The primary motor cortex are commonly held to lack layer 4, however this is currently controversial. These cells correspond to the quasi-layer 4 neurons found in a thin laminar zone at the L3/5A of the primary motor cortex that have been previously described.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_1000000> "L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex")
EquivalentClasses(<http://purl.obolibrary.org/obo/PCL_1000000> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/CL_4023008> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002100> <http://purl.obolibrary.org/obo/UBERON_0001384>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002100> <http://purl.obolibrary.org/obo/UBERON_0005393>)))

# Class: <http://purl.obolibrary.org/obo/PCL_1000002> (L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus))

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.")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:33184512"^^xsd:string) <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.")
AnnotationAssertion(dce:contributor <http://purl.obolibrary.org/obo/PCL_1000002> <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/PCL_1000002> "L2/3 PV-like SST Mus")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_1000002> "L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
Expand All @@ -151,17 +154,24 @@ SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> ObjectSomeValuesFrom(<ht
SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002215> <http://purl.obolibrary.org/obo/GO_0061534>))
SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000002> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002292> <http://purl.obolibrary.org/obo/PR_P60041>))

# Class: <http://purl.obolibrary.org/obo/PCL_1000003> (basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus))

AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:33184512"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/PCL_1000003> "A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology.")
AnnotationAssertion(dce:contributor <http://purl.obolibrary.org/obo/PCL_1000003> <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/PCL_1000003> "basket L2/3 PV-like SST (Mus)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_1000003> "basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000003> <http://purl.obolibrary.org/obo/PCL_1000002>)
SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000003> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/PATO_0070002>))

# Class: <http://purl.obolibrary.org/obo/PCL_1000004> (Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus))

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.")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "PMID:33184512"^^xsd:string) <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.")
AnnotationAssertion(dce:contributor <http://purl.obolibrary.org/obo/PCL_1000004> <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/PCL_1000004> "Martinotti L2/3 PV-like SST (Mus)")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/PCL_1000004> "Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000004> <http://purl.obolibrary.org/obo/PCL_1000002>)
SubClassOf(<http://purl.obolibrary.org/obo/PCL_1000004> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000053> <http://purl.obolibrary.org/obo/PATO_0070007>))

# Class: <http://purl.obolibrary.org/obo/SO_0001260>


AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000028> "symbol")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015001> "has exemplar data")
Expand Down