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Merge branch 'master' into 2873-ntr-smooth-muscle-circular-layer-cell…
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…-general-grouping-term
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@JABelfiore
JABelfiore authored Jan 9, 2025
2 parents 8a256ae + 304ea59 commit 22fbbda
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1 change: 1 addition & 0 deletions docs/cl-release.md
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Expand Up @@ -44,6 +44,7 @@ The release is done in two parts:
1. Ensure you are on the master branch and have locally the latest changes from master (`git pull`)
1. Ensure you have the latest ODK installed by running `docker pull obolibrary/odkfull`
1. Navigate to the cell-ontology/src/ontology directory (`cd src/ontology`)
1. Delete all temporary files (e.g., outdated plugins) by running `sh run.sh make clean`

### Refresh imports and components

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29 changes: 20 additions & 9 deletions src/ontology/cl-edit.owl
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Expand Up @@ -3048,6 +3048,7 @@ Declaration(Class(obo:CL_4033090))
Declaration(Class(obo:CL_4033091))
Declaration(Class(obo:CL_4033092))
Declaration(Class(obo:CL_4033093))
Declaration(Class(obo:CL_4033094))
Declaration(Class(obo:CL_4040000))
Declaration(Class(obo:CL_4040001))
Declaration(Class(obo:CL_4040002))
Expand Down Expand Up @@ -3387,7 +3388,7 @@ AnnotationAssertion(rdfs:label obo:IAO_0000115 "definition")

AnnotationAssertion(rdfs:label obo:IAO_0000424 "expand expression to")

# Annotation Property: obo:IAO_0000700 (has ontology root term)
# Annotation Property: obo:IAO_0000700 (preferred_root)

AnnotationAssertion(rdfs:label obo:IAO_0000700 "preferred_root")

Expand Down Expand Up @@ -3473,15 +3474,15 @@ AnnotationAssertion(rdfs:label oboInOwl:consider "consider")

AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has_broad_synonym")

# Annotation Property: oboInOwl:hasDbXref (has cross-reference)
# Annotation Property: oboInOwl:hasDbXref (database_cross_reference)

AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "database_cross_reference")

# Annotation Property: oboInOwl:hasExactSynonym (has exact synonym)
# Annotation Property: oboInOwl:hasExactSynonym (has_exact_synonym)

AnnotationAssertion(rdfs:label oboInOwl:hasExactSynonym "has_exact_synonym")

# Annotation Property: oboInOwl:hasNarrowSynonym (has narrow synonym)
# Annotation Property: oboInOwl:hasNarrowSynonym (has_narrow_synonym)

AnnotationAssertion(rdfs:label oboInOwl:hasNarrowSynonym "has_narrow_synonym")

Expand Down Expand Up @@ -24396,10 +24397,11 @@ SubClassOf(obo:CL_0011019 obo:CL_0000077)

# Class: obo:CL_0011020 (neural progenitor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30574073") obo:IAO_0000115 obo:CL_0011020 "An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:23064725") Annotation(oboInOwl:hasDbXref "PMID:30574073") Annotation(oboInOwl:hasDbXref "PMID:37508487") obo:IAO_0000115 obo:CL_0011020 "An undifferentiated cell derived from a neural stem cell, with a limited capacity to self-renew (Dibajnia and Morshead, 2013) and the ability to generate multiple types of lineage-restricted progenitors, contributing to the formation of neurons, astrocytes, and oligodendrocytes.")
AnnotationAssertion(terms:contributor obo:CL_0011020 <https://orcid.org/0000-0001-5208-3432>)
AnnotationAssertion(rdfs:label obo:CL_0011020 "neural progenitor cell")
SubClassOf(obo:CL_0011020 obo:CL_0000055)
SubClassOf(obo:CL_0011020 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000047))

# Class: obo:CL_0011021 (fibroblast of upper back skin)

Expand Down Expand Up @@ -28851,14 +28853,13 @@ AnnotationAssertion(rdfs:label obo:CL_2000056 "Meynert cell")
SubClassOf(obo:CL_2000056 obo:CL_0000598)
SubClassOf(obo:CL_2000056 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001384))

# Class: obo:CL_2000057 (femural osteoblast)
# Class: obo:CL_2000057 (femoral osteoblast)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") obo:IAO_0000115 obo:CL_2000057 "Any osteoblast that is part of a femur.")
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:TermGenie") Annotation(oboInOwl:hasDbXref "PMID:34565180") Annotation(oboInOwl:hasDbXref "PMID:34569806") obo:IAO_0000115 obo:CL_2000057 "Any osteoblast that is part of a femur.")
AnnotationAssertion(terms:contributor obo:CL_2000057 <http://www.wikidata.org/entity/Q35563349>)
AnnotationAssertion(oboInOwl:creation_date obo:CL_2000057 "2014-10-06T19:29:45Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:id obo:CL_2000057 "CL:2000057")
AnnotationAssertion(rdfs:comment obo:CL_2000057 "http://www.sciencellonline.com/site/productInformation.php?keyword=4610")
AnnotationAssertion(rdfs:label obo:CL_2000057 "femural osteoblast")
AnnotationAssertion(rdfs:label obo:CL_2000057 "femoral osteoblast")
EquivalentClasses(obo:CL_2000057 ObjectIntersectionOf(obo:CL_0000062 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000981)))

# Class: obo:CL_2000058 (calvarial osteoblast)
Expand Down Expand Up @@ -32414,6 +32415,16 @@ SubClassOf(obo:CL_4033093 obo:CL_0000036)
SubClassOf(obo:CL_4033093 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000482))
SubClassOf(obo:CL_4033093 ObjectSomeValuesFrom(obo:RO_0002203 obo:CL_0000575))

# Class: obo:CL_4033094 (age-associated B cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30873171") Annotation(oboInOwl:hasDbXref "PMID:31986068") Annotation(oboInOwl:hasDbXref "PMID:35298565") Annotation(oboInOwl:hasDbXref "PMID:35798993") obo:IAO_0000115 obo:CL_4033094 "A transcriptionally distinct memory B cell whose presence increases with age, during infections, and in autoimmune diseases. In humans and mice, this cell type can be identified by the expression of T-bet, CD11c, CD11b, and the lack of CD21. An age-associated B cell responds to TLR stimuli, may produce autoantibodies, and participates in antiviral responses and pathogen clearance.")
AnnotationAssertion(terms:contributor obo:CL_4033094 <https://orcid.org/0000-0001-6677-8489>)
AnnotationAssertion(terms:contributor obo:CL_4033094 <https://orcid.org/0000-0001-7655-4833>)
AnnotationAssertion(terms:date obo:CL_4033094 "2025-01-08T14:44:57Z"^^xsd:dateTime)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35798993") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033094 "ABC")
AnnotationAssertion(rdfs:label obo:CL_4033094 "age-associated B cell")
SubClassOf(obo:CL_4033094 obo:CL_0000787)

# Class: obo:CL_4040000 (glial restricted tripotential precursor cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10719353") obo:IAO_0000115 obo:CL_4040000 "A glial precursor cell that generates oligodendrocytes and type-1 and type-2 astrocytes. It has been shown in some mammals that this cell type may express A2B5, nestin, FGFR-1, FGFR-2, FGFR-3, PLP, and DM-20 antigens. Unlike oligodendrocyte precursor cell, it does not initially express PDGFR-alpha and can differentiate into both type-1 and type-2 astrocytes.")
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