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Merge branch 'master' into cl-pcl-product
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@shawntanzk
shawntanzk committed Jan 4, 2023
2 parents d223631 + 3d9f199 commit 1aa2261
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23 changes: 16 additions & 7 deletions .github/workflows/diff.yml
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Original file line number Diff line number Diff line change
@@ -1,16 +1,14 @@
name: 'Create ROBOT diffs on Pull requests'

on:
# Triggers the workflow on pull request events for the master branch
pull_request:
branches: [ master ]
on:

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
issue_comment:
types: [created]

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
edit_file:
if: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odklite:v1.3.0
steps:
Expand All @@ -20,8 +18,13 @@ jobs:
trigger: '#gogoeditdiff'
env:
GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
- uses: xt0rted/pull-request-comment-branch@v1
id: comment-branch
- uses: actions/checkout@v3
if: steps.check.outputs.triggered == 'true'
with:
ref: ${{ steps.comment-branch.outputs.head_ref }}
path: branch
# Checks-out main branch under "main" directory
- uses: actions/checkout@v3
if: steps.check.outputs.triggered == 'true'
Expand All @@ -30,14 +33,15 @@ jobs:
path: master
- name: Diff classification
if: steps.check.outputs.triggered == 'true'
run: export ROBOT_JAVA_ARGS=-Xmx6G; robot diff --labels True --left master/src/ontology/cl-edit.owl --left-catalog master/src/ontology/catalog-v001.xml --right src/ontology/cl-edit.owl --right-catalog src/ontology/catalog-v001.xml -f markdown -o edit-diff.md
run: export ROBOT_JAVA_ARGS=-Xmx6G; robot diff --labels True --left master/src/ontology/cl-edit.owl --left-catalog master/src/ontology/catalog-v001.xml --right branch/src/ontology/cl-edit.owl --right-catalog branch/src/ontology/catalog-v001.xml -f markdown -o edit-diff.md
- name: Upload diff
if: steps.check.outputs.triggered == 'true'
uses: actions/upload-artifact@v2
with:
name: edit-diff.md
path: edit-diff.md
classify_branch:
if: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odklite:v1.3.0
steps:
Expand All @@ -47,8 +51,12 @@ jobs:
trigger: '#gogoeditdiff'
env:
GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
- uses: xt0rted/pull-request-comment-branch@v1
id: comment-branch
- uses: actions/checkout@v3
if: steps.check.outputs.triggered == 'true'
with:
ref: ${{ steps.comment-branch.outputs.head_ref }}
- name: Classify ontology
if: steps.check.outputs.triggered == 'true'
run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE cl-simple.owl
Expand All @@ -60,6 +68,7 @@ jobs:
path: src/ontology/cl-simple.owl
retention-days: 1
classify_main:
if: ${{ github.event.issue.pull_request }}
runs-on: ubuntu-latest
container: obolibrary/odklite:v1.3.0
steps:
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112 changes: 112 additions & 0 deletions src/ontology/cl-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -2768,6 +2768,7 @@ Declaration(Class(obo:CL_4023033))
Declaration(Class(obo:CL_4023034))
Declaration(Class(obo:CL_4023036))
Declaration(Class(obo:CL_4023038))
Declaration(Class(obo:CL_4023039))
Declaration(Class(obo:CL_4023040))
Declaration(Class(obo:CL_4023041))
Declaration(Class(obo:CL_4023042))
Expand All @@ -2785,17 +2786,29 @@ Declaration(Class(obo:CL_4023053))
Declaration(Class(obo:CL_4023054))
Declaration(Class(obo:CL_4023055))
Declaration(Class(obo:CL_4023056))
Declaration(Class(obo:CL_4023057))
Declaration(Class(obo:CL_4023058))
Declaration(Class(obo:CL_4023059))
Declaration(Class(obo:CL_4023060))
Declaration(Class(obo:CL_4023061))
Declaration(Class(obo:CL_4023062))
Declaration(Class(obo:CL_4023063))
Declaration(Class(obo:CL_4023064))
Declaration(Class(obo:CL_4023065))
Declaration(Class(obo:CL_4023066))
Declaration(Class(obo:CL_4023067))
Declaration(Class(obo:CL_4023068))
Declaration(Class(obo:CL_4023069))
Declaration(Class(obo:CL_4023070))
Declaration(Class(obo:CL_4023071))
Declaration(Class(obo:CL_4023072))
Declaration(Class(obo:CL_4023073))
Declaration(Class(obo:CL_4023074))
Declaration(Class(obo:CL_4023075))
Declaration(Class(obo:CL_4023076))
Declaration(Class(obo:CL_4023077))
Declaration(Class(obo:CL_4023078))
Declaration(Class(obo:CL_4023079))
Declaration(Class(obo:CL_4023080))
Declaration(Class(obo:CL_4023081))
Declaration(Class(obo:CL_4023083))
Expand Down Expand Up @@ -29162,6 +29175,13 @@ AnnotationAssertion(oboInOwl:inSubset obo:CL_4023038 <http://purl.obolibrary.org
AnnotationAssertion(rdfs:label obo:CL_4023038 "L6b glutamatergic cortical neuron")
EquivalentClasses(obo:CL_4023038 ObjectIntersectionOf(obo:CL_0000679 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_8440003)))

# Class: obo:CL_4023039 (amgydala excitatory neuron)

AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023039 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) rdfs:comment obo:CL_4023039 "An excitatory neuron that is located in the amygdala.")
AnnotationAssertion(rdfs:label obo:CL_4023039 "amgydala excitatory neuron")
EquivalentClasses(obo:CL_4023039 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001876) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061535)))

# Class: obo:CL_4023040 (L2/3-6 intratelencephalic projecting glutamatergic cortical neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2020.10.19.343129"^^xsd:string) obo:IAO_0000115 obo:CL_4023040 "A intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layers L2/3-6")
Expand Down Expand Up @@ -29349,13 +29369,70 @@ SubClassOf(Annotation(oboInOwl:hasDbXref "PMID:30096314"^^xsd:string) obo:CL_402
SubClassOf(Annotation(oboInOwl:hasDbXref "PMID:30096314"^^xsd:string) obo:CL_4023056 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_P26618))
SubClassOf(Annotation(oboInOwl:hasDbXref "PMID:30096314"^^xsd:string) obo:CL_4023056 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_P51885))

# Class: obo:CL_4023057 (cerebellar inhibitory GABAergic interneuron)

AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023057 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) rdfs:comment obo:CL_4023057 "A GABAergic interneuron whose soma is located in the cerebellar cortex.")
AnnotationAssertion(rdfs:label obo:CL_4023057 "cerebellar inhibitory GABAergic interneuron")
EquivalentClasses(obo:CL_4023057 ObjectIntersectionOf(obo:CL_0011005 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002129)))

# Class: obo:CL_4023058 (mesothelial fibroblast of the leptomeninx)

AnnotationAssertion(obo:IAO_0000115 obo:CL_4023058 "A mesothelial fibroblast found in the leptomeninx.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023058 <https://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023058 "mesothelial fibroblast of the leptomeninx")
EquivalentClasses(obo:CL_4023058 ObjectIntersectionOf(obo:CL_4023054 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000391)))

# Class: obo:CL_4023059 (differentiation-committed oligodendrocyte precursor)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32066987"^^xsd:string) obo:IAO_0000115 obo:CL_4023059 "An oligodendrocyte precursor cell that is committed to differentiate.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023059 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(Annotation(oboInOwl:hasSynonymType <http://purl.obolibrary.org/obo/cl#abbreviation>) oboInOwl:hasExactSynonym obo:CL_4023059 "COP")
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023059 "committed oligodendrocyte precursor")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:27284195"^^xsd:string) rdfs:comment obo:CL_4023059 "COPs are distinct from OPCs in that the lack expression of Pdgfra and Cspg4 and come out as distinct clusters in transcriptomic profiling. This is the reason that this term is not modelled as a subclassOf OPC but instead linked using develops_from.")
AnnotationAssertion(rdfs:label obo:CL_4023059 "differentiation-committed oligodendrocyte precursor")
SubClassOf(obo:CL_4023059 obo:CL_0000123)
SubClassOf(obo:CL_4023059 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0002453))

# Class: obo:CL_4023060 (hippocampal CA1-3 neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023060 "A neuron that has its soma located in CA1-3 of the hippocampus.")
AnnotationAssertion(obo:IAO_0000116 obo:CL_4023060 "It is unclear as to if the modelling of Ammon's horn includes CA4 (which could be considered part of the dentate gyrus) in Uberon, hence no equivalent class axiom was made.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023060 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023060 "hippocampal CA1-3 neuron")
SubClassOf(obo:CL_4023060 obo:CL_0000540)
SubClassOf(obo:CL_4023060 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001954))

# Class: obo:CL_4023061 (hippocampal CA4 neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023061 "A neuron that has its soma located in CA4 of the hippocampus.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023061 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023061 "hippocampal CA4 neuron")
SubClassOf(obo:CL_4023061 obo:CL_0000540)

# Class: obo:CL_4023062 (dentate gyrus neuron)

AnnotationAssertion(obo:IAO_0000115 obo:CL_4023062 "A neuron with its soma located in the dentate gyrus of the hippocampus.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023062 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023062 "dentate gyrus neuron")
EquivalentClasses(obo:CL_4023062 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001885)))

# Class: obo:CL_4023063 (medial ganglionic eminence derived interneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023063 "An interneuron that is derived from the medial ganglionic eminence.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023063 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023063 "MGE interneuron")
AnnotationAssertion(rdfs:label obo:CL_4023063 "medial ganglionic eminence derived interneuron")
EquivalentClasses(obo:CL_4023063 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002202 obo:UBERON_0004024)))

# Class: obo:CL_4023064 (caudal ganglionic eminence derived interneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023064 "An interneuron that is derived from the caudal ganglionic eminence.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023064 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023064 "CGE interneuron")
AnnotationAssertion(rdfs:label obo:CL_4023064 "caudal ganglionic eminence derived interneuron")
EquivalentClasses(obo:CL_4023064 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002202 obo:UBERON_0004026)))

# Class: obo:CL_4023065 (meis2 expressing cortical GABAergic cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33372656"^^xsd:string) obo:IAO_0000115 obo:CL_4023065 "A GABAergic cell located in the cerebral cortex that expresses meis2.")
Expand Down Expand Up @@ -29384,6 +29461,13 @@ AnnotationAssertion(rdfs:comment obo:CL_4023067 "Moved to PCL - see https://gith
AnnotationAssertion(rdfs:label obo:CL_4023067 "obsolete Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
AnnotationAssertion(owl:deprecated obo:CL_4023067 "true"^^xsd:boolean)

# Class: obo:CL_4023068 (thalamic excitatory neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023068 "An excitatory neuron that has its soma located in the thalamic complex.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023068 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023068 "thalamic excitatory neuron")
EquivalentClasses(obo:CL_4023068 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0010225) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061535)))

# Class: obo:CL_4023069 (medial ganglionic eminence derived GABAergic cortical interneuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12637172"^^xsd:string) obo:IAO_0000115 obo:CL_4023069 "A GABAergic cortical interneuron that develops from the medial ganglionic eminence and has migrated to the cerebral cortex.")
Expand Down Expand Up @@ -29413,6 +29497,27 @@ SubClassOf(obo:CL_4023071 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_1009
SubClassOf(obo:CL_4023071 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0061534))
SubClassOf(obo:CL_4023071 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_P09240))

# Class: obo:CL_4023072 (brain vascular cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023072 "A cell that is part of the brain vasculature.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023072 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023072 "brain vascular cell")
EquivalentClasses(obo:CL_4023072 ObjectIntersectionOf(obo:CL_0000003 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008998)))

# Class: obo:CL_4023073 (choroid plexus cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023073 "A cell that is part of the choroid plexus.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023073 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023073 "choroid plexus cell")
EquivalentClasses(obo:CL_4023073 ObjectIntersectionOf(obo:CL_0000003 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001886)))

# Class: obo:CL_4023074 (mammillary body neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023074 "A neuron that has its soma located in the mammillary body.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023074 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023074 "mammillary body neuron")
EquivalentClasses(obo:CL_4023074 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002206)))

# Class: obo:CL_4023075 (L6 tyrosine hydroxylase sst GABAergic cortical interneuron (Mmus))

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:22357664"^^xsd:string) obo:IAO_0000115 obo:CL_4023075 "A sst GABAergic cortical interneuron found in L6 that expresses tyrosine hydroxylase. L6 Th+ SST cells have mostly local axonal arborization within L6.")
Expand Down Expand Up @@ -29457,6 +29562,13 @@ AnnotationAssertion(rdfs:comment obo:CL_4023078 "Moved to PCL - see https://gith
AnnotationAssertion(rdfs:label obo:CL_4023078 "obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)")
AnnotationAssertion(owl:deprecated obo:CL_4023078 "true"^^xsd:boolean)

# Class: obo:CL_4023079 (midbrain-derived inhibitory neuron)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1101/2022.10.12.511898"^^xsd:string) obo:IAO_0000115 obo:CL_4023079 "A GABAergic inhibitory neuron that is derived from the midbrain.")
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4023079 <http://orcid.org/0000-0001-7258-9596>)
AnnotationAssertion(rdfs:label obo:CL_4023079 "midbrain-derived inhibitory neuron")
EquivalentClasses(obo:CL_4023079 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002202 obo:UBERON_0001891)))

# Class: obo:CL_4023080 (stellate L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex (Mmus))

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9236245"^^xsd:string) obo:IAO_0000115 obo:CL_4023080 "a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has stellate pyramidal morphology.")
Expand Down

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