From f96ced6fc5395a06ed212961a99d0f58e8414781 Mon Sep 17 00:00:00 2001 From: CEastwood <116108977+Caroline-99@users.noreply.github.com> Date: Tue, 1 Oct 2024 13:14:30 +0100 Subject: [PATCH] Fixes #2528 - NTRs - externa and interna theca cells (#2622) * Fixes #2528 -Added two new terms - interna and exerna theca cells -Added textual, logical defs, references and synonyms -imported uberon terms -revised the logical and textual defs of theca cells * Update cl-edit.owl * Update cl-edit.owl --- src/ontology/cl-edit.owl | 34 +++++++++++++-- src/ontology/imports/merged_import.owl | 60 +++++++++++++++++++++++++- src/ontology/imports/uberon_terms.txt | 4 +- src/patterns/definitions.owl | 4 +- 4 files changed, 94 insertions(+), 8 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 0b91d5306..4b66ea957 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3091,6 +3091,8 @@ Declaration(Class(obo:CL_4052008)) Declaration(Class(obo:CL_4052009)) Declaration(Class(obo:CL_4052010)) Declaration(Class(obo:CL_4052011)) +Declaration(Class(obo:CL_4052012)) +Declaration(Class(obo:CL_4052013)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -3179,6 +3181,8 @@ Declaration(Class(obo:PR_Q96E93)) Declaration(Class(obo:PR_Q9D387)) Declaration(Class(obo:PR_Q9Y5Y4)) Declaration(Class(obo:PR_Q9Z0F7)) +Declaration(Class(obo:UBERON_0000156)) +Declaration(Class(obo:UBERON_0000157)) Declaration(Class(obo:UBERON_0000371)) Declaration(Class(obo:UBERON_0000424)) Declaration(Class(obo:UBERON_0001004)) @@ -7737,11 +7741,11 @@ SubClassOf(obo:CL_0000502 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0070253)) # Class: obo:CL_0000503 (theca cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D013799") obo:IAO_0000115 obo:CL_0000503 "A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D013799") Annotation(oboInOwl:hasDbXref "PMID:36758341") Annotation(oboInOwl:hasDbXref "PMID:15833266") obo:IAO_0000115 obo:CL_0000503 "A specialized stromal cell that forms the theca layer outside the basal lamina lining the ovarian follicle, appearing during the secondary follicle stage.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000503 "BTO:0002850") AnnotationAssertion(rdfs:label obo:CL_0000503 "theca cell") SubClassOf(obo:CL_0000503 obo:CL_0000499) -SubClassOf(obo:CL_0000503 obo:CL_0000593) +SubClassOf(obo:CL_0000503 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000155)) SubClassOf(obo:CL_0000503 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001305)) # Class: obo:CL_0000504 (enterochromaffin-like cell) @@ -32580,7 +32584,7 @@ EquivalentClasses(obo:CL_4047052 ObjectIntersectionOf(obo:CL_1000347 ObjectSomeV # Class: obo:CL_4047101 (liver-resident natural killer cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26330348") Annotation(oboInOwl:hasDbXref "PMID:26639736") Annotation(oboInOwl:hasDbXref "PMID:27798170") Annotation(oboInOwl:hasDbXref "PMID:32351704") Annotation(oboInOwl:hasDbXref "PMID:34230995") Annotation(oboInOwl:hasDbXref "PMID:35865550") Annotation(oboInOwl:hasDbXref "PMID:31114585") obo:IAO_0000115 obo:CL_4047101 "A natural killer cell resident to the liver, located in the hepatic sinusoids. In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26330348") Annotation(oboInOwl:hasDbXref "PMID:26639736") Annotation(oboInOwl:hasDbXref "PMID:27798170") Annotation(oboInOwl:hasDbXref "PMID:31114585") Annotation(oboInOwl:hasDbXref "PMID:32351704") Annotation(oboInOwl:hasDbXref "PMID:34230995") Annotation(oboInOwl:hasDbXref "PMID:35865550") obo:IAO_0000115 obo:CL_4047101 "A natural killer cell resident to the liver, located in the hepatic sinusoids. In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans.") AnnotationAssertion(terms:contributor obo:CL_4047101 ) AnnotationAssertion(terms:contributor obo:CL_4047101 "https://orcid.org/0000-0001-8134-3037") AnnotationAssertion(terms:date obo:CL_4047101 "2024-07-29T13:43:11Z"^^xsd:dateTime) @@ -32727,6 +32731,30 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:7107724") oboInOwl:hasRe AnnotationAssertion(rdfs:label obo:CL_4052011 "follicle associated enterocyte") SubClassOf(obo:CL_4052011 obo:CL_0000584) +# Class: obo:CL_4052012 (interna theca cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31320652") Annotation(oboInOwl:hasDbXref "PMID:32530882") Annotation(oboInOwl:hasDbXref "Wikipedia:Theca_interna") Annotation(oboInOwl:hasDbXref "PMID:15833266") obo:IAO_0000115 obo:CL_4052012 "A specialized theca cell that forms the inner, highly vascularized layer of the theca surrounding ovarian follicles. Originating from progenitor theca cells, the theca interna cell is steroidogenic, playing a crucial role in the production of androgens, which serves as a precursor for estrogen synthesis in granulosa cells. This cell expresses luteinizing hormone receptors, enabling it to respond to hormonal signals that regulate steroidogenesis.") +AnnotationAssertion(terms:contributor obo:CL_4052012 ) +AnnotationAssertion(terms:date obo:CL_4052012 "2024-09-30T11:10:15Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31320652") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052012 "inTC") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31320652") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052012 "interna TC") +AnnotationAssertion(rdfs:label obo:CL_4052012 "interna theca cell") +EquivalentClasses(obo:CL_4052012 ObjectIntersectionOf(obo:CL_0000503 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000157))) +SubClassOf(obo:CL_4052012 obo:CL_0000593) +SubClassOf(obo:CL_4052012 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4052010)) +DisjointClasses(obo:CL_4052012 obo:CL_4052013) + +# Class: obo:CL_4052013 (externa theca cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31320652") Annotation(oboInOwl:hasDbXref "PMID:32530882") Annotation(oboInOwl:hasDbXref "PMID:36758341") Annotation(oboInOwl:hasDbXref "Wikipedia:Theca_externa") obo:IAO_0000115 obo:CL_4052013 "A specialized theca cell that forms the outer layer of the theca surrounding the ovarian follicle, appearing at the antral follicle. Originating from progenitor theca cells, theca externa cell is characterized by its fibroblast-like appearance and primarily function to provide structural support to the developing follicle. This cell produces collagen fibers and extracellular matrix components such as Col1a1 and Col1a2.") +AnnotationAssertion(terms:contributor obo:CL_4052013 ) +AnnotationAssertion(terms:date obo:CL_4052013 "2024-09-30T11:10:15Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31320652") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052013 "exTC") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31320652") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4052013 "externa TC") +AnnotationAssertion(rdfs:label obo:CL_4052013 "externa theca cell") +EquivalentClasses(obo:CL_4052013 ObjectIntersectionOf(obo:CL_0000503 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000156))) +SubClassOf(obo:CL_4052013 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_4052010)) + # 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/merged_import.owl b/src/ontology/imports/merged_import.owl index 28932b487..3307b731c 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-09-25") + +Annotation(owl:versionInfo "2024-09-30") Declaration(Class()) Declaration(Class()) @@ -9252,6 +9252,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -133636,6 +133638,60 @@ SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (theca externa) + +AnnotationAssertion(Annotation( "Wikipedia:Theca_externa") "The theca externa is the outer layers of the theca folliculi. It contains abundant collagen and is mainly supportive.") +AnnotationAssertion( ) +AnnotationAssertion( "UBERON:0005182") +AnnotationAssertion( "BTO:0002852") +AnnotationAssertion( "FMA:18657") +AnnotationAssertion( "MA:0001713") +AnnotationAssertion( "SCTID:258767003") +AnnotationAssertion( "Wikipedia:Theca_externa") +AnnotationAssertion(Annotation( "MA:0001713") "ovary theca externa") +AnnotationAssertion(Annotation( "FMA:18657") "theca externa (folliculus ovaricus tertiarius)") +AnnotationAssertion(Annotation( "FMA:18657") "tunica externa of theca folliculi") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "BTO:0002852") "external coat of theca folliculi") +AnnotationAssertion(Annotation( "BTO:0002852") Annotation( "Wikipedia:Theca_externa") Annotation( ) "tunica externa thecae folliculi") +AnnotationAssertion( "UBERON:0000156") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "theca externa") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/5/50/Mature_Graffian_follicle.jpg"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (theca interna) + +AnnotationAssertion(Annotation( "Wikipedia:Theca_externa#Theca_interna") "Theca interna cells express receptors for luteinizing hormone, which when activated will stimulate the production of androstenedione from cholesterol by the enzyme desmolase. Androstenedione ultimately gives the granulosa cells the precursor substrate for estrogen manufacturing.") +AnnotationAssertion( ) +AnnotationAssertion( "UBERON:0005183") +AnnotationAssertion( "BTO:0002851") +AnnotationAssertion( "FMA:18658") +AnnotationAssertion( "MA:0001714") +AnnotationAssertion( "SCTID:258869006") +AnnotationAssertion( "Wikipedia:Theca_externa#Theca_interna") +AnnotationAssertion(Annotation( "MA:0001714") "ovary theca interna") +AnnotationAssertion(Annotation( "FMA:18658") "theca interna (folliculus ovaricus tertiarius)") +AnnotationAssertion(Annotation( "FMA:18658") "tunica interna of theca folliculi") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "BTO:0002851") "internal coat of capsule of Graafian follicle") +AnnotationAssertion(Annotation( "BTO:0002851") "tunica interna thecae folliculi") +AnnotationAssertion( "UBERON:0000157") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "theca interna") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (membranous layer) AnnotationAssertion( "membrane") diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index 4c558184c..44e4e4599 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -56,4 +56,6 @@ UBERON:0014727 UBERON:0014729 UBERON:0013739 UBERON:0013740 -UBERON:0012186 \ No newline at end of file +UBERON:0012186 +UBERON:0000156 +UBERON:0000157 \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 5455e8867..ed8ae81e6 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-09-25") + +Annotation(owl:versionInfo "2024-09-30") Declaration(Class()) Declaration(Class())