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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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53 changes: 45 additions & 8 deletions src/ontology/bdso-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,15 @@ 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>))
Expand All @@ -46,6 +48,7 @@ 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:license))
Expand All @@ -54,6 +57,31 @@ Declaration(AnnotationProperty(dcterms:provenance))
Declaration(AnnotationProperty(dcterms:description))
Declaration(AnnotationProperty(dcterms:subject))
Declaration(AnnotationProperty(dcterms:relation))


############################
# Object Properties
############################

# Object Property: <http://purl.obolibrary.org/obo/RO_0002100> (has soma location)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002100> "has soma location")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002215> (capable of)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002215> "capable of")

# Object Property: <http://purl.obolibrary.org/obo/RO_0002292> (expresses)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0002292> "expresses")

# Object Property: <http://purl.obolibrary.org/obo/RO_0015001> (has exemplar data)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015001> "has exemplar data")

# Object Property: <http://purl.obolibrary.org/obo/RO_0015002> (exemplar data of)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015002> "exemplar data of")

# Object Property: <http://purl.obolibrary.org/obo/RO_0015003> (subcluster of)
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/RO_0015003> "subcluster of")


############################
# Annotation Properties
############################
Expand Down Expand Up @@ -129,14 +157,14 @@ 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") <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(dce:creator <http://purl.obolibrary.org/obo/PCL_1000000> <http://orcid.org/0000-0001-7258-9596>)
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@shawntanzk shawntanzk Feb 16, 2022 •
edited
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this should be dc:contributor

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> "These cells likely corresponded to the quasi-L4 neurons described previously in the motor cortex.")
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explain l4 issue here

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_4023040> 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>)))
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equiv class is wrong


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

Expand All @@ -151,6 +179,15 @@ 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.")
Expand Down