From 91f1519bf74660260aa4f8f60427dd64df6ac1bf Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Fri, 10 Jan 2025 10:50:20 +0000 Subject: [PATCH 1/2] Fixes #2875 NTR-granzyme H-associated CD8 T cell Added a new term --- src/ontology/cl-edit.owl | 13 +++++++++++++ src/ontology/imports/pr_terms.txt | 3 ++- 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 4b5f159fc..6ca60308b 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)) @@ -33490,6 +33492,17 @@ 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), significantly expanded in systemic lupus erythematosus (SLE) patients. This cell exhibits a restricted TCR repertoire and elevated expression of cytotoxic, exhaustion, and type I interferon-stimulated gene signatures compared to controls. Unlike other CD8 T cell populations, GZMH+ CD8 T cells can comprise up to 50% of all lymphocytes in some SLE patients.") +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(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.") diff --git a/src/ontology/imports/pr_terms.txt b/src/ontology/imports/pr_terms.txt index 697340509..4c403c315 100644 --- a/src/ontology/imports/pr_terms.txt +++ b/src/ontology/imports/pr_terms.txt @@ -50,4 +50,5 @@ PR:000016626 PR:000003472 PR:000012318 PR:000064867 -PR:000001440 \ No newline at end of file +PR:000001440 +PR:000003490 \ No newline at end of file From b1938f14f07362ef276c0e278da63af94ee7076a Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Fri, 10 Jan 2025 12:00:05 +0000 Subject: [PATCH 2/2] Update cl-edit.owl --- src/ontology/cl-edit.owl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 6ca60308b..b60fcc0af 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -33494,12 +33494,13 @@ SubClassOf(obo:CL_4052031 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000205 # 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), significantly expanded in systemic lupus erythematosus (SLE) patients. This cell exhibits a restricted TCR repertoire and elevated expression of cytotoxic, exhaustion, and type I interferon-stimulated gene signatures compared to controls. Unlike other CD8 T cell populations, GZMH+ CD8 T cells can comprise up to 50% of all lymphocytes in some SLE patients.") +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)))