From b687bb9a5a17f9df6ff871086949143478d67e04 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 14:32:54 +0100 Subject: [PATCH 1/4] Adresses #2179 NTR lactocyte subtypes Adresses #2179 NTR lactocyte subtypes --- src/ontology/cl-edit.owl | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 587067836..bc4aab013 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3003,6 +3003,8 @@ Declaration(Class(obo:CL_4033053)) Declaration(Class(obo:CL_4033054)) Declaration(Class(obo:CL_4033055)) Declaration(Class(obo:CL_4033056)) +Declaration(Class(obo:CL_4033059)) +Declaration(Class(obo:CL_4033060)) Declaration(Class(obo:CL_4040000)) Declaration(Class(obo:CL_4040001)) Declaration(Class(obo:CL_4040002)) @@ -31685,6 +31687,31 @@ AnnotationAssertion(rdfs:label obo:CL_4033056 "onychocyte") SubClassOf(obo:CL_4033056 obo:CL_0000312) SubClassOf(obo:CL_4033056 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008198)) +# Class: obo:CL_4033059 (lactocyte type 1) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasDbXref "PMID:35377806") obo:IAO_0000115 obo:CL_4033059 "A lactocyte that highly expresses genes associated with transcription, immune cell function, and cellular stress. A lactocyte type 1 also expresses genes involved in milk component biosynthesis (e.g., LALBA and CSNs), albeit at lower levels than a lactocyte type 2.") +AnnotationAssertion( obo:CL_4033059 ) +AnnotationAssertion( obo:CL_4033059 ) +AnnotationAssertion( obo:CL_4033059 "2023-10-16T13:15:36Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35377806") oboInOwl:hasBroadSynonym obo:CL_4033059 "luminal cluster 1 cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033059 "LC1") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") oboInOwl:hasRelatedSynonym obo:CL_4033059 "LMC major luminal cluster 1") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033059 "progenitor MEC") +AnnotationAssertion(rdfs:label obo:CL_4033059 "lactocyte type 1") +SubClassOf(obo:CL_4033059 obo:CL_0002325) + +# Class: obo:CL_4033060 (lactocyte type 2) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasDbXref "PMID:35377806") obo:IAO_0000115 obo:CL_4033060 "A lactocyte that highly expresses genes associated with lipid production and milk component biosynthesis, suggesting that this cell type is more mature than a lactocyte type 1.") +AnnotationAssertion( obo:CL_4033060 ) +AnnotationAssertion( obo:CL_4033060 ) +AnnotationAssertion( obo:CL_4033060 "2023-10-16T13:15:55Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033060 "LC2") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") oboInOwl:hasRelatedSynonym obo:CL_4033060 "LMC major luminal cluster 2") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35377806") oboInOwl:hasRelatedSynonym obo:CL_4033060 "luminal cluster 2 cell") +AnnotationAssertion(rdfs:label obo:CL_4033060 "lactocyte type 2") +SubClassOf(obo:CL_4033060 obo:CL_0002325) + # 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.") From ce3c639f2ed796383c4fded0a1b7305b1ee1bc5b Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 17:50:52 +0100 Subject: [PATCH 2/4] Corrected dbxref for progenitor MEC --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index bc4aab013..26902e682 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31693,7 +31693,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(ob AnnotationAssertion( obo:CL_4033059 ) AnnotationAssertion( obo:CL_4033059 ) AnnotationAssertion( obo:CL_4033059 "2023-10-16T13:15:36Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35377806") oboInOwl:hasBroadSynonym obo:CL_4033059 "luminal cluster 1 cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34097179") oboInOwl:hasBroadSynonym obo:CL_4033059 "luminal cluster 1 cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033059 "LC1") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") oboInOwl:hasRelatedSynonym obo:CL_4033059 "LMC major luminal cluster 1") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033059 "progenitor MEC") From 98fe9e573e62eeba2d71c2d6b2250e42cbfb185a Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 17:52:56 +0100 Subject: [PATCH 3/4] Corrected synonym type --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 26902e682..0700a3999 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31706,9 +31706,9 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(ob AnnotationAssertion( obo:CL_4033060 ) AnnotationAssertion( obo:CL_4033060 ) AnnotationAssertion( obo:CL_4033060 "2023-10-16T13:15:55Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35377806") oboInOwl:hasBroadSynonym obo:CL_4033060 "luminal cluster 2 cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033060 "LC2") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") oboInOwl:hasRelatedSynonym obo:CL_4033060 "LMC major luminal cluster 2") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35377806") oboInOwl:hasRelatedSynonym obo:CL_4033060 "luminal cluster 2 cell") AnnotationAssertion(rdfs:label obo:CL_4033060 "lactocyte type 2") SubClassOf(obo:CL_4033060 obo:CL_0002325) From 3fc59f220ed55b5103e6825a90009e98cfe3c7a8 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 17:56:07 +0100 Subject: [PATCH 4/4] Remove uncertain sentence --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 0700a3999..ebdf286bf 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31702,7 +31702,7 @@ SubClassOf(obo:CL_4033059 obo:CL_0002325) # Class: obo:CL_4033060 (lactocyte type 2) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasDbXref "PMID:35377806") obo:IAO_0000115 obo:CL_4033060 "A lactocyte that highly expresses genes associated with lipid production and milk component biosynthesis, suggesting that this cell type is more mature than a lactocyte type 1.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35091553") Annotation(oboInOwl:hasDbXref "PMID:35377806") obo:IAO_0000115 obo:CL_4033060 "A lactocyte that highly expresses genes associated with lipid production and milk component biosynthesis.") AnnotationAssertion( obo:CL_4033060 ) AnnotationAssertion( obo:CL_4033060 ) AnnotationAssertion( obo:CL_4033060 "2023-10-16T13:15:55Z"^^xsd:dateTime)