From db33925b64ca72d8cb796855417f69231f1ed2b2 Mon Sep 17 00:00:00 2001 From: CEastwood <116108977+Caroline-99@users.noreply.github.com> Date: Wed, 8 Jan 2025 13:06:18 +0000 Subject: [PATCH 1/4] Fixes #2806 Femoral osteoblast (#2879) - Fixed typo in the label - Added references for the cell type - removed a broken link in the comment section --- src/ontology/cl-edit.owl | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 6c65df477..ecdd448ad 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -28850,14 +28850,13 @@ 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 ) 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) From c6a8a74bbde5e81ba98c3dc6a907340afbc57255 Mon Sep 17 00:00:00 2001 From: CEastwood <116108977+Caroline-99@users.noreply.github.com> Date: Wed, 8 Jan 2025 14:01:57 +0000 Subject: [PATCH 2/4] Fixes #2807 text and logical def- neural progenitor cell (#2881) - Fixed the textual def and added references -Added developmental logical axiom --- src/ontology/cl-edit.owl | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index ecdd448ad..7699d525f 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3386,7 +3386,7 @@ 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") @@ -3472,15 +3472,15 @@ 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") @@ -24395,10 +24395,11 @@ 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:30574073") Annotation(oboInOwl:hasDbXref "PMID:23064725") 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 ) 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) From 5a8888a4ed458c8a2d7dc78ea25239cda9868056 Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Wed, 8 Jan 2025 14:50:54 +0000 Subject: [PATCH 3/4] Add step to clean temporary files (#2883) --- docs/cl-release.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/cl-release.md b/docs/cl-release.md index af966ac3f..7209cfb2c 100644 --- a/docs/cl-release.md +++ b/docs/cl-release.md @@ -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 From 304ea5942529c4a716fc321d2a9649bde21a8d2a Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 9 Jan 2025 10:08:49 +0000 Subject: [PATCH 4/4] Adresses #2791 NTR age-associated cell (#2884) Fixes #2791 NTR age-associated cell Co-authored-by: CEastwood <116108977+Caroline-99@users.noreply.github.com> --- src/ontology/cl-edit.owl | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 7699d525f..44b685703 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -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)) @@ -24395,7 +24396,7 @@ SubClassOf(obo:CL_0011019 obo:CL_0000077) # Class: obo:CL_0011020 (neural progenitor cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30574073") Annotation(oboInOwl:hasDbXref "PMID:23064725") 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(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 ) AnnotationAssertion(rdfs:label obo:CL_0011020 "neural progenitor cell") SubClassOf(obo:CL_0011020 obo:CL_0000055) @@ -32413,6 +32414,16 @@ 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 ) +AnnotationAssertion(terms:contributor obo:CL_4033094 ) +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.")