From 4b77c185fd1a03d879d648370379a11caacccf8a Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Tue, 24 Sep 2024 16:16:24 +0100 Subject: [PATCH 1/2] definition --- src/ontology/cl-edit.owl | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 94d1b506b..5ba53c68e 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3070,6 +3070,7 @@ Declaration(Class(obo:CL_4047006)) Declaration(Class(obo:CL_4047007)) Declaration(Class(obo:CL_4047011)) Declaration(Class(obo:CL_4047012)) +Declaration(Class(obo:CL_4047022)) Declaration(Class(obo:CL_4047051)) Declaration(Class(obo:CL_4047052)) Declaration(Class(obo:CL_4052001)) @@ -32454,6 +32455,16 @@ AnnotationAssertion(terms:date obo:CL_4047012 "2024-09-06T08:41:39Z"^^xsd:dateTi AnnotationAssertion(rdfs:label obo:CL_4047012 "angiogenic pericyte"@en) SubClassOf(obo:CL_4047012 obo:CL_0000669) +# Class: obo:CL_4047022 (mesenchymal lymphoid tissue organizer cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31201308") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047022 "A stromal cell found in the adult gut that plays a crucial role in the formation and maintenance of gut-associated lymphoid tissues (GALTs). This cell is characterized by it's ability to interact with lymphoid tissue inducer (LTi) cells, express lymphotoxin beta receptor (LTβR) and vascular cell adhesion molecule (VCAM), produce chemokines and cytokines for immune cell recruitment and positioning, and contribute to the structural organization of lymphoid tissues within the intestinal environment. mLTo cells are distinguished from other stromal cells by their specific function in orchestrating the development and maintenance of organized lymphoid structures in the gut, which are essential for intestinal immune responses and homeostasis.") +AnnotationAssertion(terms:contributor obo:CL_4047022 ) +AnnotationAssertion(terms:date obo:CL_4047022 "2024-09-24T15:03:49Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31201308") oboInOwl:hasExactSynonym obo:CL_4047022 "mLTo cells") +AnnotationAssertion(rdfs:label obo:CL_4047022 "mesenchymal lymphoid tissue organizer cell"@en) +EquivalentClasses(obo:CL_4047022 ObjectIntersectionOf(obo:CL_0000134 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001962))) +SubClassOf(obo:CL_4047022 obo:CL_0000134) + # Class: obo:CL_4047051 (small intestine BEST4+ enterocyte) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24223998") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047051 "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium.") From 89f37033111255676ba51d0c5bd5712786c4c793 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Thu, 7 Nov 2024 16:13:58 +0000 Subject: [PATCH 2/2] DOI update --- src/ontology/cl-edit.owl | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index daeb1cc4c..55ec5549e 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3102,6 +3102,7 @@ Declaration(Class(obo:GO_0036053)) Declaration(Class(obo:GO_0036376)) Declaration(Class(obo:GO_0042599)) Declaration(Class(obo:GO_0044316)) +Declaration(Class(obo:GO_0051767)) Declaration(Class(obo:GO_0070278)) Declaration(Class(obo:GO_0070483)) Declaration(Class(obo:GO_0097729)) @@ -3146,8 +3147,8 @@ Declaration(Class(obo:PR_000007479)) Declaration(Class(obo:PR_000007489)) Declaration(Class(obo:PR_000007785)) Declaration(Class(obo:PR_000009981)) -Declaration(Class(obo:PR_000013047)) Declaration(Class(obo:PR_000010529)) +Declaration(Class(obo:PR_000013047)) Declaration(Class(obo:PR_000013502)) Declaration(Class(obo:PR_000014419)) Declaration(Class(obo:PR_000014898)) @@ -32493,10 +32494,10 @@ SubClassOf(obo:CL_4047012 obo:CL_0000669) # Class: obo:CL_4047022 (mesenchymal lymphoid tissue organizer cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31201308") Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047022 "A stromal cell found in the adult gut that plays a crucial role in the formation and maintenance of gut-associated lymphoid tissues (GALTs). This cell is characterized by it's ability to interact with lymphoid tissue inducer (LTi) cells, express lymphotoxin beta receptor (LTβR) and vascular cell adhesion molecule (VCAM), produce chemokines and cytokines for immune cell recruitment and positioning, and contribute to the structural organization of lymphoid tissues within the intestinal environment. mLTo cells are distinguished from other stromal cells by their specific function in orchestrating the development and maintenance of organized lymphoid structures in the gut, which are essential for intestinal immune responses and homeostasis.") +AnnotationAssertion(Annotation(obo:IAO_0000115 "DOI:10.4049/jimmunol.1501724") Annotation(oboInOwl:hasDbXref "DOI:10.1038/s41586-021-03852-1") obo:IAO_0000115 obo:CL_4047022 "A stromal cell found in the adult gut that plays a crucial role in the formation and maintenance of gut-associated lymphoid tissues (GALTs). This cell is characterized by it's ability to interact with lymphoid tissue inducer (LTi) cells, express lymphotoxin beta receptor (LTβR) and vascular cell adhesion molecule (VCAM), produce chemokines and cytokines for immune cell recruitment and positioning, and contribute to the structural organization of lymphoid tissues within the intestinal environment. mLTo cells are distinguished from other stromal cells by their specific function in orchestrating the development and maintenance of organized lymphoid structures in the gut, which are essential for intestinal immune responses and homeostasis.") AnnotationAssertion(terms:contributor obo:CL_4047022 ) AnnotationAssertion(terms:date obo:CL_4047022 "2024-09-24T15:03:49Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31201308") oboInOwl:hasExactSynonym obo:CL_4047022 "mLTo cells") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "DOI:10.1038/s41467-019-09728-3") oboInOwl:hasExactSynonym obo:CL_4047022 "mLTo cells") AnnotationAssertion(rdfs:label obo:CL_4047022 "mesenchymal lymphoid tissue organizer cell"@en) EquivalentClasses(obo:CL_4047022 ObjectIntersectionOf(obo:CL_0000134 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001962))) SubClassOf(obo:CL_4047022 obo:CL_0000134)