From f40a912ac9be926cf9e2b64df9de248fbf33a9c4 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Fri, 10 Jan 2025 16:09:44 +0000 Subject: [PATCH 1/4] M cell and FAE partonomy update --- src/ontology/cl-edit.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 4b5f159fc..d176e96d9 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -9457,7 +9457,7 @@ SubClassOf(obo:CL_0000676 obo:CL_0000378) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "JB:jb") obo:IAO_0000115 obo:CL_0000677 "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.") AnnotationAssertion(rdfs:label obo:CL_0000677 "gut absorptive cell") SubClassOf(obo:CL_0000677 obo:CL_0000000) -SubClassOf(obo:CL_0000677 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001277)) +SubClassOf(obo:CL_0000677 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693)) # Class: obo:CL_0000678 (commissural neuron) @@ -9506,7 +9506,7 @@ AnnotationAssertion(rdfs:label obo:CL_0000682 "M cell of gut") SubClassOf(obo:CL_0000682 obo:CL_0000066) SubClassOf(obo:CL_0000682 obo:CL_0000473) SubClassOf(obo:CL_0000682 obo:CL_0000627) -SubClassOf(obo:CL_0000682 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003929)) +SubClassOf(obo:CL_0000682 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693)) # Class: obo:CL_0000683 (ependymoglial cell) From fc6eb1a2e47c03be58f09d053f703fff4ee19ebf Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Mon, 13 Jan 2025 14:32:24 +0000 Subject: [PATCH 2/4] partonomy gut absorptive cell update 'part of' some 'intestinal epithelium' --- src/ontology/cl-edit.owl | 16 +--------------- 1 file changed, 1 insertion(+), 15 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index f3769f40a..b213f1562 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3145,7 +3145,6 @@ Declaration(Class(obo:CL_4052028)) Declaration(Class(obo:CL_4052029)) Declaration(Class(obo:CL_4052030)) Declaration(Class(obo:CL_4052031)) -Declaration(Class(obo:CL_4052032)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -3207,7 +3206,6 @@ Declaration(Class(obo:PR_000002030)) Declaration(Class(obo:PR_000002123)) Declaration(Class(obo:PR_000003264)) Declaration(Class(obo:PR_000003472)) -Declaration(Class(obo:PR_000003490)) Declaration(Class(obo:PR_000004691)) Declaration(Class(obo:PR_000004919)) Declaration(Class(obo:PR_000005444)) @@ -9459,7 +9457,7 @@ SubClassOf(obo:CL_0000676 obo:CL_0000378) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "JB:jb") obo:IAO_0000115 obo:CL_0000677 "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules.") AnnotationAssertion(rdfs:label obo:CL_0000677 "gut absorptive cell") SubClassOf(obo:CL_0000677 obo:CL_0000000) -SubClassOf(obo:CL_0000677 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693)) +SubClassOf(obo:CL_0000677 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001277)) # Class: obo:CL_0000678 (commissural neuron) @@ -33492,18 +33490,6 @@ AnnotationAssertion(rdfs:label obo:CL_4052031 "respiratory airway secretory cell SubClassOf(obo:CL_4052031 obo:CL_1100001) SubClassOf(obo:CL_4052031 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002051)) -# Class: obo:CL_4052032 (granzyme H-associated CD8 T cell) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") obo:IAO_0000115 obo:CL_4052032 "A CD8 T cell characterized by high expression of Granzyme H (GZMH). This cell exhibits a restricted TCR repertoire and elevated expression of cytotoxic, exhaustion, and type I interferon-stimulated gene signatures compared to controls.") -AnnotationAssertion(terms:contributor obo:CL_4052032 ) -AnnotationAssertion(terms:contributor obo:CL_4052032 ) -AnnotationAssertion(terms:date obo:CL_4052032 "2025-01-10T10:14:31Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") oboInOwl:hasExactSynonym obo:CL_4052032 "granzyme H+ CD8 T cell") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052032 "GZMH+ CD8+ T cell") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") rdfs:comment obo:CL_4052032 "This cell type is significantly expanded in systemic lupus erythematosus (SLE) patients. Unlike other CD8 T cell populations, GZMH+ CD8 T cells can comprise up to 50% of all lymphocytes in some SLE patients.") -AnnotationAssertion(rdfs:label obo:CL_4052032 "granzyme H-associated CD8 T cell") -EquivalentClasses(obo:CL_4052032 ObjectIntersectionOf(obo:CL_0000909 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000003490))) - # Class: obo:CL_4052048 (intercalated cell of salivary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.") From d9a2bf763b16f99028319b6bf618a3a94cfba93a Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Tue, 14 Jan 2025 14:17:51 +0000 Subject: [PATCH 3/4] partonomy update FAE --- 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 b213f1562..55ed5d095 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -33270,7 +33270,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") oboInOwl:hasEx AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052011 "FAE enterocyte") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") oboInOwl:hasRelatedSynonym obo:CL_4052011 "follicular enterocyte") AnnotationAssertion(rdfs:label obo:CL_4052011 "follicle associated enterocyte") -SubClassOf(obo:CL_4052011 obo:CL_0000584) +EquivalentClasses(obo:CL_4052011 ObjectIntersectionOf(obo:CL_0000584 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693))) # Class: obo:CL_4052012 (interna theca cell) From d6c41405c572f636b06e600690f6f2af32c0440d Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Fri, 17 Jan 2025 15:13:06 +0000 Subject: [PATCH 4/4] Modified the partonomy and added the deleted term --- src/ontology/cl-edit.owl | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 55ed5d095..e24e52b67 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3145,6 +3145,7 @@ Declaration(Class(obo:CL_4052028)) Declaration(Class(obo:CL_4052029)) Declaration(Class(obo:CL_4052030)) Declaration(Class(obo:CL_4052031)) +Declaration(Class(obo:CL_4052032)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -3206,6 +3207,7 @@ Declaration(Class(obo:PR_000002030)) Declaration(Class(obo:PR_000002123)) Declaration(Class(obo:PR_000003264)) Declaration(Class(obo:PR_000003472)) +Declaration(Class(obo:PR_000003490)) Declaration(Class(obo:PR_000004691)) Declaration(Class(obo:PR_000004919)) Declaration(Class(obo:PR_000005444)) @@ -33270,7 +33272,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") oboInOwl:hasEx AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052011 "FAE enterocyte") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") oboInOwl:hasRelatedSynonym obo:CL_4052011 "follicular enterocyte") AnnotationAssertion(rdfs:label obo:CL_4052011 "follicle associated enterocyte") -EquivalentClasses(obo:CL_4052011 ObjectIntersectionOf(obo:CL_0000584 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693))) +SubClassOf(obo:CL_4052011 obo:CL_0000584) +SubClassOf(obo:CL_4052011 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004693)) # Class: obo:CL_4052012 (interna theca cell) @@ -33490,6 +33493,18 @@ AnnotationAssertion(rdfs:label obo:CL_4052031 "respiratory airway secretory cell SubClassOf(obo:CL_4052031 obo:CL_1100001) SubClassOf(obo:CL_4052031 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002051)) +# Class: obo:CL_4052032 (granzyme H-associated CD8 T cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") obo:IAO_0000115 obo:CL_4052032 "A CD8 T cell characterized by high expression of Granzyme H (GZMH). This cell exhibits a restricted TCR repertoire and elevated expression of cytotoxic, exhaustion, and type I interferon-stimulated gene signatures compared to controls.") +AnnotationAssertion(terms:contributor obo:CL_4052032 ) +AnnotationAssertion(terms:contributor obo:CL_4052032 ) +AnnotationAssertion(terms:date obo:CL_4052032 "2025-01-10T10:14:31Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") oboInOwl:hasExactSynonym obo:CL_4052032 "granzyme H+ CD8 T cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052032 "GZMH+ CD8+ T cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35389781") rdfs:comment obo:CL_4052032 "This cell type is significantly expanded in systemic lupus erythematosus (SLE) patients. Unlike other CD8 T cell populations, GZMH+ CD8 T cells can comprise up to 50% of all lymphocytes in some SLE patients.") +AnnotationAssertion(rdfs:label obo:CL_4052032 "granzyme H-associated CD8 T cell") +EquivalentClasses(obo:CL_4052032 ObjectIntersectionOf(obo:CL_0000909 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000003490))) + # Class: obo:CL_4052048 (intercalated cell of salivary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30855909") Annotation(oboInOwl:hasDbXref "PMID:35799078") Annotation(oboInOwl:hasDbXref "PMID:36726292") Annotation(oboInOwl:hasDbXref "PMID:37724716") obo:IAO_0000115 obo:CL_4052048 "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption.")