From 3e268876d013e457263e82fca15de01cf011148f Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Thu, 12 Oct 2023 15:59:50 +0100 Subject: [PATCH 1/2] Addresses #2154 [NTR] IT projecting glu cortical neurons by layer --- src/ontology/cl-edit.owl | 78 +++++++++++++++++++++++++++++++++++++--- 1 file changed, 74 insertions(+), 4 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 934a3c23d..b36b93b20 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -2937,6 +2937,13 @@ Declaration(Class(obo:CL_4030055)) Declaration(Class(obo:CL_4030056)) Declaration(Class(obo:CL_4030057)) Declaration(Class(obo:CL_4030058)) +Declaration(Class(obo:CL_4030059)) +Declaration(Class(obo:CL_4030060)) +Declaration(Class(obo:CL_4030061)) +Declaration(Class(obo:CL_4030062)) +Declaration(Class(obo:CL_4030063)) +Declaration(Class(obo:CL_4030064)) +Declaration(Class(obo:CL_4030065)) Declaration(Class(obo:CL_4032000)) Declaration(Class(obo:CL_4032001)) Declaration(Class(obo:CL_4033000)) @@ -29464,7 +29471,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023047 "L2/3 IT M1") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023047 "L2/3 IT MOp") AnnotationAssertion(oboInOwl:inSubset obo:CL_4023047 ) AnnotationAssertion(rdfs:label obo:CL_4023047 "L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") -EquivalentClasses(obo:CL_4023047 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384) ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_8440000))) +EquivalentClasses(obo:CL_4023047 ObjectIntersectionOf(obo:CL_4030059 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384))) # Class: obo:CL_4023048 (L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex) @@ -29476,7 +29483,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023048 "L4/5 IT M1") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023048 "L4/5 IT MOp") AnnotationAssertion(oboInOwl:inSubset obo:CL_4023048 ) AnnotationAssertion(rdfs:label obo:CL_4023048 "L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") -EquivalentClasses(obo:CL_4023048 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384) ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_8440001))) +EquivalentClasses(obo:CL_4023048 ObjectIntersectionOf(obo:CL_4030062 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384))) # Class: obo:CL_4023049 (L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex) @@ -29488,7 +29495,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023049 "L5 IT M1") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023049 "L5 IT MOp") AnnotationAssertion(oboInOwl:inSubset obo:CL_4023049 ) AnnotationAssertion(rdfs:label obo:CL_4023049 "L5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") -EquivalentClasses(obo:CL_4023049 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384) ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005394))) +EquivalentClasses(obo:CL_4023049 ObjectIntersectionOf(obo:CL_4030064 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384))) # Class: obo:CL_4023050 (L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex) @@ -29500,7 +29507,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023050 "L6 IT M1") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023050 "L6 IT MOp") AnnotationAssertion(oboInOwl:inSubset obo:CL_4023050 ) AnnotationAssertion(rdfs:label obo:CL_4023050 "L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") -EquivalentClasses(obo:CL_4023050 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384) ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005395))) +EquivalentClasses(obo:CL_4023050 ObjectIntersectionOf(obo:CL_4030065 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384))) SubClassOf(obo:CL_4023050 ObjectSomeValuesFrom(obo:RO_0000053 obo:PATO_0070019)) # Class: obo:CL_4023051 (vascular leptomeningeal cell) @@ -31035,6 +31042,69 @@ AnnotationAssertion(Annotation(oboInOwl:SynonymTypeProperty obo:OMO_0003000) Ann AnnotationAssertion(rdfs:label obo:CL_4030058 "TCR-positive macrophage") EquivalentClasses(obo:CL_4030058 ObjectIntersectionOf(obo:CL_0000235 ObjectSomeValuesFrom(obo:RO_0002104 obo:GO_0042101))) +# Class: obo:CL_4030059 (L2/3 intratelencephalic projecting glutamatergic neuron) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34004146") Annotation(oboInOwl:hasDbXref "PMID:37292694") obo:IAO_0000115 obo:CL_4030059 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3.") +AnnotationAssertion( obo:CL_4030059 ) +AnnotationAssertion( obo:CL_4030059 "2023-10-10T14:10:21Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34004146") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4030059 "L2/3 IT") +AnnotationAssertion(rdfs:label obo:CL_4030059 "L2/3 intratelencephalic projecting glutamatergic neuron") +EquivalentClasses(obo:CL_4030059 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_8440000))) + +# Class: obo:CL_4030060 (L2 intratelencephalic projecting glutamatergic neuron) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34004146") obo:IAO_0000115 obo:CL_4030060 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2.") +AnnotationAssertion( obo:CL_4030060 ) +AnnotationAssertion( obo:CL_4030060 "2023-10-10T14:10:36Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34004146") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4030060 "L2 IT") +AnnotationAssertion(rdfs:label obo:CL_4030060 "L2 intratelencephalic projecting glutamatergic neuron") +EquivalentClasses(obo:CL_4030060 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005391))) + +# Class: obo:CL_4030061 (L3 intratelencephalic projecting glutamatergic neuron) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34004146") obo:IAO_0000115 obo:CL_4030061 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 3.") +AnnotationAssertion( obo:CL_4030061 ) +AnnotationAssertion( obo:CL_4030061 "2023-10-10T14:10:47Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34004146") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4030061 "L3 IT") +AnnotationAssertion(rdfs:label obo:CL_4030061 "L3 intratelencephalic projecting glutamatergic neuron") +EquivalentClasses(obo:CL_4030061 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005392))) + +# Class: obo:CL_4030062 (L4/5 intratelencephalic projecting glutamatergic neuron) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34004146") obo:IAO_0000115 obo:CL_4030062 "An intratelencephalic-projecting glutamatergic with a soma located in cortical layer 4/5.") +AnnotationAssertion( obo:CL_4030062 ) +AnnotationAssertion( obo:CL_4030062 "2023-10-10T14:11:04Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34004146") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4030062 "L4/5 IT") +AnnotationAssertion(rdfs:label obo:CL_4030062 "L4/5 intratelencephalic projecting glutamatergic neuron") +EquivalentClasses(obo:CL_4030062 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_8440001))) + +# Class: obo:CL_4030063 (L4 intratelencephalic projecting glutamatergic neuron) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") obo:IAO_0000115 obo:CL_4030063 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4.") +AnnotationAssertion( obo:CL_4030063 ) +AnnotationAssertion( obo:CL_4030063 "2023-10-10T14:11:25Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4030063 "L4 IT") +AnnotationAssertion(rdfs:label obo:CL_4030063 "L4 intratelencephalic projecting glutamatergic neuron") +EquivalentClasses(obo:CL_4030063 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005393))) + +# Class: obo:CL_4030064 (L5 intratelencephalic projecting glutamatergic neuron) + +AnnotationAssertion( obo:CL_4030064 ) +AnnotationAssertion( obo:CL_4030064 "2023-10-10T14:11:59Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasDbXref "PMID:37609206") oboInOwl:hasDbXref obo:CL_4030064 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5.") +AnnotationAssertion(Annotation(oboInOwl:SynonymTypeProperty obo:OMO_0003000) Annotation(oboInOwl:hasDbXref "PMID:37292694") oboInOwl:hasRelatedSynonym obo:CL_4030064 "L5 IT") +AnnotationAssertion(rdfs:label obo:CL_4030064 "L5 intratelencephalic projecting glutamatergic neuron") +EquivalentClasses(obo:CL_4030064 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005394))) + +# Class: obo:CL_4030065 (L6 intratelencephalic projecting glutamatergic neuron) + +AnnotationAssertion( obo:CL_4030065 ) +AnnotationAssertion( obo:CL_4030065 "2023-10-10T14:12:23Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasDbXref "PMID:37609206") oboInOwl:hasDbXref obo:CL_4030065 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4030065 "L6 IT") +AnnotationAssertion(rdfs:label obo:CL_4030065 "L6 intratelencephalic projecting glutamatergic neuron") +EquivalentClasses(obo:CL_4030065 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005395))) + # Class: obo:CL_4032000 (club-like cell of the urethral epithelium) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30566875") Annotation(oboInOwl:hasDbXref "PMID:32497356") obo:IAO_0000115 obo:CL_4032000 "An epithelial cell of the urethra that has an expression profile similar to lung club cells. Club-like cells of the urethra epithelium are similar to lung club cells in their expression of SCGB1A1 and in their enrichment of immunomodulatory programs.") From 29c33ca8f674932708f36ae5ad856507a254ff9a Mon Sep 17 00:00:00 2001 From: bvarner-ebi <95643797+bvarner-ebi@users.noreply.github.com> Date: Fri, 13 Oct 2023 09:04:26 +0100 Subject: [PATCH 2/2] Update cl-edit.owl fix def annotation --- src/ontology/cl-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index b36b93b20..587067836 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31089,18 +31089,18 @@ EquivalentClasses(obo:CL_4030063 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeV # Class: obo:CL_4030064 (L5 intratelencephalic projecting glutamatergic neuron) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasDbXref "PMID:37609206") obo:IAO_0000115 obo:CL_4030064 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5.") AnnotationAssertion( obo:CL_4030064 ) AnnotationAssertion( obo:CL_4030064 "2023-10-10T14:11:59Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasDbXref "PMID:37609206") oboInOwl:hasDbXref obo:CL_4030064 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5.") AnnotationAssertion(Annotation(oboInOwl:SynonymTypeProperty obo:OMO_0003000) Annotation(oboInOwl:hasDbXref "PMID:37292694") oboInOwl:hasRelatedSynonym obo:CL_4030064 "L5 IT") AnnotationAssertion(rdfs:label obo:CL_4030064 "L5 intratelencephalic projecting glutamatergic neuron") EquivalentClasses(obo:CL_4030064 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005394))) # Class: obo:CL_4030065 (L6 intratelencephalic projecting glutamatergic neuron) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasDbXref "PMID:37609206") obo:IAO_0000115 obo:CL_4030065 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6.") AnnotationAssertion( obo:CL_4030065 ) AnnotationAssertion( obo:CL_4030065 "2023-10-10T14:12:23Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasDbXref "PMID:37609206") oboInOwl:hasDbXref obo:CL_4030065 "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6.") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37292694") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4030065 "L6 IT") AnnotationAssertion(rdfs:label obo:CL_4030065 "L6 intratelencephalic projecting glutamatergic neuron") EquivalentClasses(obo:CL_4030065 ObjectIntersectionOf(obo:CL_4023040 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0005395)))