From 099282ef4d695c421b3df926530363afbde5b615 Mon Sep 17 00:00:00 2001 From: Caroline Eastwood Date: Wed, 25 Sep 2024 13:23:20 +0100 Subject: [PATCH] Fixes #2527 - Added a new term with logical, textual defs, synonyms and refs --- src/ontology/cl-edit.owl | 16 ++++- src/ontology/imports/merged_import.owl | 88 +++++++++++++++++++++++++- src/ontology/imports/uberon_terms.txt | 3 +- src/patterns/definitions.owl | 4 +- 4 files changed, 105 insertions(+), 6 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index f414ba55d..897d082c7 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3083,6 +3083,7 @@ Declaration(Class(obo:CL_4052006)) Declaration(Class(obo:CL_4052007)) Declaration(Class(obo:CL_4052008)) Declaration(Class(obo:CL_4052009)) +Declaration(Class(obo:CL_4052010)) Declaration(Class(obo:CL_4052048)) Declaration(Class(obo:CL_4052049)) Declaration(Class(obo:CP_0000000)) @@ -3145,8 +3146,8 @@ 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)) @@ -3206,6 +3207,7 @@ Declaration(Class(obo:UBERON_0009852)) Declaration(Class(obo:UBERON_0010397)) Declaration(Class(obo:UBERON_0011184)) Declaration(Class(obo:UBERON_0011949)) +Declaration(Class(obo:UBERON_0012186)) Declaration(Class(obo:UBERON_0012398)) Declaration(Class(obo:UBERON_0012399)) Declaration(Class(obo:UBERON_0012419)) @@ -32614,6 +32616,18 @@ AnnotationAssertion(rdfs:label obo:CL_4052009 "crypt-top fibroblast") SubClassOf(obo:CL_4052009 obo:CL_4052007) SubClassOf(obo:CL_4052009 ObjectSomeValuesFrom(obo:RO_0002220 obo:UBERON_0013740)) +# Class: obo:CL_4052010 (pre-theca cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20628033") Annotation(oboInOwl:hasDbXref "PMID:31320652") Annotation(oboInOwl:hasDbXref "PMID:36205477") obo:IAO_0000115 obo:CL_4052010 "A stromal cell that serves as a precursor to the theca cell layers in the ovary growing follicles. This cell is present in the early stages of follicular growth, particularly in smaller follicles, and gradually differentiates into theca interna and theca externa cells as the follicle matures. Unlike mature theca cell, pre-theca cell is initially non-steroidogenic and lacks luteinizing hormone receptors.") +AnnotationAssertion(terms:contributor obo:CL_4052010 ) +AnnotationAssertion(terms:date obo:CL_4052010 "2024-09-25T11:15:57Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36205477") oboInOwl:hasExactSynonym obo:CL_4052010 "early theca cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31320652") oboInOwl:hasExactSynonym obo:CL_4052010 "progenitor theca cell") +AnnotationAssertion(rdfs:label obo:CL_4052010 "pre-theca cell") +SubClassOf(obo:CL_4052010 obo:CL_0000499) +SubClassOf(obo:CL_4052010 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0012186)) +SubClassOf(obo:CL_4052010 ObjectSomeValuesFrom(obo:RO_0002203 obo:CL_0000503)) + # 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 4278d16e8..28932b487 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 "2024-09-24") + +Annotation(owl:versionInfo "2024-09-25") Declaration(Class()) Declaration(Class()) @@ -8627,6 +8627,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8677,6 +8678,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8841,6 +8843,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8911,6 +8914,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12932,6 +12936,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -120927,6 +120932,21 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "prolactin") SubClassOf( ) +# Class: (parathyroid hormone-related protein) + +AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human PTHLH gene or a 1:1 ortholog thereof.") +AnnotationAssertion( "PTH-rP") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "PTHLH") +AnnotationAssertion( "PTHrP") +AnnotationAssertion( "parathyroid hormone-like protein") +AnnotationAssertion( "protein") +AnnotationAssertion( "PLP") +AnnotationAssertion(Annotation( ) "PTHRP") +AnnotationAssertion( "PR:000013433") +AnnotationAssertion(rdfs:comment "Category=gene.") +AnnotationAssertion(rdfs:label "parathyroid hormone-related protein") +SubClassOf( ) + # Class: (parvalbumin alpha) AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human PVALB gene or a 1:1 ortholog thereof.") @@ -121602,6 +121622,19 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (parathyroid hormone-related protein proteolytic cleavage product) + +AnnotationAssertion(Annotation( "PRO:DNx") "A parathyroid hormone-related protein that has been processed by proteolytic cleavage.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "PTHLH/ClvPrd") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000021172") +AnnotationAssertion(rdfs:comment "Category=modification.") +AnnotationAssertion(rdfs:label "parathyroid hormone-related protein proteolytic cleavage product") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (sonic hedgehog protein proteolytic cleavage product) AnnotationAssertion(Annotation( "PRO:DNx") "A sonic hedgehog protein that has been processed by proteolytic cleavage.") @@ -124482,6 +124515,25 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (parathyroid hormone-related protein (human)) + +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:P12272") "A parathyroid hormone-related protein that is encoded in the genome of human.") +AnnotationAssertion(Annotation( "UniProtKB:P12272") "PLP (human)") +AnnotationAssertion( "UniProtKB:P12272") +AnnotationAssertion(Annotation( "UniProtKB:P12272") "PTH-rP (human)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hPTHLH") +AnnotationAssertion(Annotation( "UniProtKB:P12272") "parathyroid hormone-like protein (human)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:P12272") Annotation( ) "PTHLH") +AnnotationAssertion(Annotation( "UniProtKB:P12272") Annotation( ) "PTHRP") +AnnotationAssertion( "PR:P12272") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "parathyroid hormone-related protein (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (high affinity immunoglobulin gamma Fc receptor I (human)) AnnotationAssertion(Annotation( "PRO:CNA") Annotation( "UniProtKB:P12314") "A high affinity immunoglobulin gamma Fc receptor I that is encoded in the genome of human.") @@ -125924,6 +125976,26 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (parathyroid hormone-related protein (mouse)) + +AnnotationAssertion(Annotation( "OMA:P22858") Annotation( "PRO:DNx") "A parathyroid hormone-related protein that is encoded in the genome of mouse.") +AnnotationAssertion( "UniProtKB:P22858") +AnnotationAssertion(Annotation( "UniProtKB:P22858") "PTH-rP (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P22858") "PTHrP (mouse)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mPTHLH") +AnnotationAssertion(Annotation( "UniProtKB:P22858") "parathyroid hormone-like protein (mouse)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:P22858") "PLP (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P22858") Annotation( ) "Pthlh") +AnnotationAssertion(Annotation( "UniProtKB:P22858") Annotation( ) "Pthrp") +AnnotationAssertion( "PR:P22858") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "parathyroid hormone-related protein (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (macrophage mannose receptor 1 (human)) AnnotationAssertion(Annotation( "PRO:CNA") Annotation( "UniProtKB:P22897") "A macrophage mannose receptor 1 that is encoded in the genome of human.") @@ -216846,6 +216918,18 @@ EquivalentClasses( ObjectIntersec SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (ovary growing follicle) + +AnnotationAssertion(Annotation( "ncithesaurus:Growing_Follicle") "An ovarian follicle undergoing maturation.") +AnnotationAssertion( "EMAPA:35628") +AnnotationAssertion( "MA:0001708") +AnnotationAssertion( "NCIT:C32702") +AnnotationAssertion(Annotation( "ncithesaurus:Growing_Follicle") "UMLS:C1512279") +AnnotationAssertion( "uberon") +AnnotationAssertion( "UBERON:0012186") +AnnotationAssertion(rdfs:label "ovary growing follicle") +SubClassOf(Annotation( "MA") ) + # Class: (phrenic vein) AnnotationAssertion(Annotation( "ncithesaurus:Phrenic_Vein") "The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins.") diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt index ff0d76541..34e9162f5 100644 --- a/src/ontology/imports/uberon_terms.txt +++ b/src/ontology/imports/uberon_terms.txt @@ -54,4 +54,5 @@ UBERON:0004642 UBERON:0006250 UBERON:0014727 UBERON:0014729 -UBERON:0013739 \ No newline at end of file +UBERON:0013739 +UBERON:0012186 \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 5fc7c7cd2..5455e8867 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-09-24") + +Annotation(owl:versionInfo "2024-09-25") Declaration(Class()) Declaration(Class())