From 228a363162ca1207ce9c6ee0b489988d3b2671cd Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Thu, 16 Dec 2021 08:50:14 +0000 Subject: [PATCH 1/5] Added L4 IT Fixes #226 Note given the rest of IT aren't species restricted, I opted to make this species agnostic too --- src/ontology/bdso-edit.owl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/src/ontology/bdso-edit.owl b/src/ontology/bdso-edit.owl index aad94427..8e5cbdfb 100644 --- a/src/ontology/bdso-edit.owl +++ b/src/ontology/bdso-edit.owl @@ -46,6 +46,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(Class()) ############################ # Object Properties @@ -109,4 +110,18 @@ AnnotationAssertion(rdfs:label "cel # Annotation Property: (nuclei_count) AnnotationAssertion(rdfs:label "nuclei_count") +############################ +# Classes +############################ + +# Class: (L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex) + +AnnotationAssertion(Annotation( "PMID:33184512") "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 ) +AnnotationAssertion( "ILX:0770172") +AnnotationAssertion(Annotation( "PMID:25525751") rdfs:comment "These cells likely corresponded to the quasi-L4 neurons described previously in the motor cortex.") +AnnotationAssertion(rdfs:label "L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + ) \ No newline at end of file From f665798989a8e7e1f6452183c06b1283aef6f64a Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Thu, 16 Dec 2021 08:58:30 +0000 Subject: [PATCH 2/5] Update bdso-edit.owl --- src/ontology/bdso-edit.owl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/ontology/bdso-edit.owl b/src/ontology/bdso-edit.owl index 8e5cbdfb..28f7e52d 100644 --- a/src/ontology/bdso-edit.owl +++ b/src/ontology/bdso-edit.owl @@ -121,7 +121,5 @@ AnnotationAssertion(dce:creator "ILX:0770172") AnnotationAssertion(Annotation( "PMID:25525751") rdfs:comment "These cells likely corresponded to the quasi-L4 neurons described previously in the motor cortex.") AnnotationAssertion(rdfs:label "L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) ) \ No newline at end of file From aff0e059eed42b07762b9ab5a961db5332b134f0 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Tue, 11 Jan 2022 10:26:53 +0000 Subject: [PATCH 3/5] Update mistake in IRI --- src/ontology/bdso-edit.owl | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/src/ontology/bdso-edit.owl b/src/ontology/bdso-edit.owl index a4b5aed1..e8415031 100644 --- a/src/ontology/bdso-edit.owl +++ b/src/ontology/bdso-edit.owl @@ -24,14 +24,15 @@ Annotation(dce:title "Brain Data Standards Cell Ontology") Annotation(dcterms:license ) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -50,6 +51,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(dce:contributor)) +Declaration(AnnotationProperty(dce:creator)) Declaration(AnnotationProperty(dce:description)) Declaration(AnnotationProperty(dce:title)) Declaration(AnnotationProperty(dcterms:license)) @@ -124,6 +126,7 @@ AnnotationAssertion(rdfs:label "cel AnnotationAssertion(rdfs:label "nuclei_count") + ############################ # Object Properties ############################ @@ -140,11 +143,12 @@ AnnotationAssertion(rdfs:label "capa AnnotationAssertion(rdfs:label "expresses") + + ############################ # Classes ############################ - # Class: (L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex) AnnotationAssertion(Annotation( "PMID:33184512") "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.") @@ -154,15 +158,6 @@ AnnotationAssertion(Annotation( "L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -# Class: (basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)) - -AnnotationAssertion(Annotation( "PMID:33184512") "A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology.") -AnnotationAssertion(dce:contributor ) -AnnotationAssertion( "basket L2/3 PV-like SST (Mus)") -AnnotationAssertion(rdfs:label "basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)) AnnotationAssertion(Annotation( "PMID:33184512") "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.") @@ -176,6 +171,15 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)) + +AnnotationAssertion(Annotation( "PMID:33184512"^^xsd:string) "A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology.") +AnnotationAssertion(dce:contributor ) +AnnotationAssertion( "basket L2/3 PV-like SST (Mus)") +AnnotationAssertion(rdfs:label "basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)) AnnotationAssertion(Annotation( "PMID:33184512") "A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology.") @@ -190,5 +194,4 @@ AnnotationAssertion(rdfs:label "sym AnnotationAssertion(rdfs:label "has exemplar data") AnnotationAssertion(rdfs:label "exemplar data of") AnnotationAssertion(rdfs:label "subcluster of") - ) \ No newline at end of file From 99119667cf04f1130bd5459fc6a75022a6c31537 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Thu, 17 Feb 2022 13:40:47 +0000 Subject: [PATCH 4/5] Update bdso-edit.owl --- src/ontology/bdso-edit.owl | 47 ++++++++------------------------------ 1 file changed, 10 insertions(+), 37 deletions(-) diff --git a/src/ontology/bdso-edit.owl b/src/ontology/bdso-edit.owl index 1a409a16..1b3b63b8 100644 --- a/src/ontology/bdso-edit.owl +++ b/src/ontology/bdso-edit.owl @@ -12,9 +12,9 @@ Ontology( Import() Import() Import() -Import() Import() Import() +Import() Annotation(dce:title "Brain Data Standards Cell Ontology") Annotation(dcterms:license ) @@ -30,8 +30,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -51,37 +51,12 @@ 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)) - - -############################ -# Object Properties -############################ - -# Object Property: (has soma location) -AnnotationAssertion(rdfs:label "has soma location") - -# Object Property: (capable of) -AnnotationAssertion(rdfs:label "capable of") - -# Object Property: (expresses) -AnnotationAssertion(rdfs:label "expresses") - -# Object Property: (has exemplar data) -AnnotationAssertion(rdfs:label "has exemplar data") - -# Object Property: (exemplar data of) -AnnotationAssertion(rdfs:label "exemplar data of") - -# Object Property: (subcluster of) -AnnotationAssertion(rdfs:label "subcluster of") - - +Declaration(AnnotationProperty(dcterms:subject)) +Declaration(AnnotationProperty(dcterms:title)) ############################ # Annotation Properties ############################ @@ -159,16 +134,16 @@ AnnotationAssertion(rdfs:label "has # Class: (L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex) -AnnotationAssertion(Annotation( "PMID:33184512") "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 ) +AnnotationAssertion(Annotation( "PMID:33184512"^^xsd:string) "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 ) AnnotationAssertion( "ILX:0770172") AnnotationAssertion(Annotation( "PMID:25525751") rdfs:comment "These cells likely corresponded to the quasi-L4 neurons described previously in the motor cortex.") AnnotationAssertion(rdfs:label "L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)) -AnnotationAssertion(Annotation( "PMID:33184512") "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( "PMID:33184512"^^xsd:string) "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 ) AnnotationAssertion( "L2/3 PV-like SST Mus") AnnotationAssertion(rdfs:label "L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)") @@ -190,15 +165,13 @@ SubClassOf( ObjectSomeValuesFrom( (Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)) -AnnotationAssertion(Annotation( "PMID:33184512") "A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology.") +AnnotationAssertion(Annotation( "PMID:33184512"^^xsd:string) "A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology.") AnnotationAssertion(dce:contributor ) AnnotationAssertion( "Martinotti L2/3 PV-like SST (Mus)") AnnotationAssertion(rdfs:label "Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: - AnnotationAssertion(rdfs:label "symbol") AnnotationAssertion(rdfs:label "has exemplar data") From 7b05945de4dba09ad7e55fd1d96866d3c1aeb350 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Thu, 17 Feb 2022 13:47:39 +0000 Subject: [PATCH 5/5] Update bdso-edit.owl --- src/ontology/bdso-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/bdso-edit.owl b/src/ontology/bdso-edit.owl index 1b3b63b8..c8aa4180 100644 --- a/src/ontology/bdso-edit.owl +++ b/src/ontology/bdso-edit.owl @@ -137,7 +137,7 @@ AnnotationAssertion(rdfs:label "has AnnotationAssertion(Annotation( "PMID:33184512"^^xsd:string) "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 ) AnnotationAssertion( "ILX:0770172") -AnnotationAssertion(Annotation( "PMID:25525751") rdfs:comment "These cells likely corresponded to the quasi-L4 neurons described previously in the motor cortex.") +AnnotationAssertion(Annotation( "PMID:25525751") rdfs:comment "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 "L4 intratelencephalic projecting glutamatergic neuron of the primary motor cortex") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))