From 8a66eea21ae42cf30e859cf637e730d15946f925 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Tue, 22 Nov 2022 10:40:16 +0100 Subject: [PATCH] Fix contributor QC (#1734) * add annotation declaration dce:contributor and run normalize_src * normalise xsd string Co-authored-by: Anita Caron --- src/ontology/cl-edit.owl | 27 ++++++++++--------- ...legal-annotation-property-violation.sparql | 6 ++--- 2 files changed, 17 insertions(+), 16 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index c78e8f2fd..e0407ece7 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -2882,6 +2882,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -15242,7 +15243,7 @@ AnnotationAssertion(oboInOwl:hasAlternativeId obo:CL_0002196 "CL:1000036"^^xsd:s AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002196 "BTO:0004270"^^xsd:string) AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0002196 "FMA:86576"^^xsd:string) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002196 "hepatic oval cell"^^xsd:string) -AnnotationAssertion(Annotation( ) Annotation(oboInOwl:hasDbXref ) oboInOwl:hasExactSynonym obo:CL_0002196 "hepatic progenitor cell"^^xsd:string) +AnnotationAssertion(Annotation( ) Annotation(oboInOwl:hasDbXref ) oboInOwl:hasExactSynonym obo:CL_0002196 "hepatic progenitor cell"^^xsd:string) AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) oboInOwl:hasExactSynonym obo:CL_0002196 "liver progenitor cell"^^xsd:string) AnnotationAssertion(rdfs:label obo:CL_0002196 "hepatic oval stem cell"^^xsd:string) SubClassOf(obo:CL_0002196 obo:CL_0011026) @@ -23053,7 +23054,7 @@ EquivalentClasses(obo:CL_0019032 ObjectIntersectionOf(obo:CL_0002204 ObjectSomeV AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24051376"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:31300091"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:32016094"^^xsd:string) obo:IAO_0000115 obo:CL_0700009 "OBSOLETE. A renal beta-intercalated cell that is part of the cortical collecting duct. The medullary collecting duct does not contain the renal beta-intercalated cell type."^^xsd:string) AnnotationAssertion(obo:IAO_0100001 obo:CL_0700009 obo:CL_4030005) -AnnotationAssertion( obo:CL_0700009 ) +AnnotationAssertion( obo:CL_0700009 ) AnnotationAssertion( obo:CL_0700009 "2022-08-26T10:31:29Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32016094"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_0700009 "B-IC"^^xsd:string) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31300091"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_0700009 "kidney collecting duct intercalated cell type B"^^xsd:string) @@ -28676,7 +28677,7 @@ SubClassOf(obo:CL_4030000 obo:CL_0000148) # Class: obo:CL_4030001 (stromal cell of thymus) AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) obo:IAO_0000115 obo:CL_4030001 "A stromal cell that is part of the thymus."^^xsd:string) -AnnotationAssertion( obo:CL_4030001 ) +AnnotationAssertion( obo:CL_4030001 ) AnnotationAssertion( obo:CL_4030001 "2022-07-08T11:39:38Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030001 "thymic stromal cell"^^xsd:string) AnnotationAssertion(rdfs:label obo:CL_4030001 "stromal cell of thymus") @@ -28698,7 +28699,7 @@ SubClassOf(obo:CL_4030002 obo:CL_0000791) # Class: obo:CL_4030003 (interstitial cell of thymus) AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) obo:IAO_0000115 obo:CL_4030003 "A cell that makes up the loose connective tissue of the thymus."^^xsd:string) -AnnotationAssertion( obo:CL_4030003 ) +AnnotationAssertion( obo:CL_4030003 ) AnnotationAssertion( obo:CL_4030003 "2022-07-08T11:48:36Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030003 "thymic interstitial cell"^^xsd:string) AnnotationAssertion(rdfs:label obo:CL_4030003 "interstitial cell of thymus") @@ -28715,7 +28716,7 @@ SubClassOf(obo:CL_4030004 obo:CL_0002293) # Class: obo:CL_4030005 (kidney collecting duct beta-intercalated cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24051376"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:31300091"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:32016094"^^xsd:string) obo:IAO_0000115 obo:CL_4030005 "A renal beta-intercalated cell that is part of the cortical collecting duct. The medullary collecting duct does not contain the renal beta-intercalated cell type."^^xsd:string) -AnnotationAssertion( obo:CL_4030005 ) +AnnotationAssertion( obo:CL_4030005 ) AnnotationAssertion( obo:CL_4030005 "2022-09-14T16:19:11Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32016094"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4030005 "B-IC"^^xsd:string) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31300091"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4030005 "kidney collecting duct intercalated cell type B"^^xsd:string) @@ -28844,7 +28845,7 @@ EquivalentClasses(obo:CL_4030017 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeV # Class: obo:CL_4030018 (kidney connecting tubule principal cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "PMID:27582101"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:31249312"^^xsd:string) obo:IAO_0000115 obo:CL_4030018 "A renal principal cell located in the connecting tubule."^^xsd:string) -AnnotationAssertion( obo:CL_4030018 ) +AnnotationAssertion( obo:CL_4030018 ) AnnotationAssertion( obo:CL_4030018 "2022-06-27T15:25:10Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4030018 "kidney connecting tubule principal cell") EquivalentClasses(obo:CL_4030018 ObjectIntersectionOf(obo:CL_0005009 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005097))) @@ -28852,7 +28853,7 @@ EquivalentClasses(obo:CL_4030018 ObjectIntersectionOf(obo:CL_0005009 ObjectSomeV # Class: obo:CL_4030019 (kidney connecting tubule intercalated cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9890303"^^xsd:string) obo:IAO_0000115 obo:CL_4030019 "A renal intercalated cell that is part of the renal connecting tubule."^^xsd:string) -AnnotationAssertion( obo:CL_4030019 ) +AnnotationAssertion( obo:CL_4030019 ) AnnotationAssertion( obo:CL_4030019 "2022-06-29T11:25:22Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4030019 "kidney connecting tubule intercalated cell") EquivalentClasses(obo:CL_4030019 ObjectIntersectionOf(obo:CL_0005010 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005097))) @@ -28861,7 +28862,7 @@ SubClassOf(obo:CL_4030019 obo:CL_1000768) # Class: obo:CL_4030020 (kidney connecting tubule alpha-intercalated cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:2254448"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:24937428"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:9890303"^^xsd:string) obo:IAO_0000115 obo:CL_4030020 "A renal alpha-intercalated cell that is part of the renal connecting tubule."^^xsd:string) -AnnotationAssertion( obo:CL_4030020 ) +AnnotationAssertion( obo:CL_4030020 ) AnnotationAssertion( obo:CL_4030020 "2022-06-29T12:48:43Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:24937428"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4030020 "connecting tubule A-IC"^^xsd:string) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9890303"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4030020 "kidney connecting tubule intercalated cell type A"^^xsd:string) @@ -28871,7 +28872,7 @@ EquivalentClasses(obo:CL_4030020 ObjectIntersectionOf(obo:CL_0005011 ObjectSomeV # Class: obo:CL_4030021 (kidney connecting tubule beta-intercalated cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:2254448"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:9890303"^^xsd:string) obo:IAO_0000115 obo:CL_4030021 "A renal beta-intercalated cell that is part of the renal connecting tubule."^^xsd:string) -AnnotationAssertion( obo:CL_4030021 ) +AnnotationAssertion( obo:CL_4030021 ) AnnotationAssertion( obo:CL_4030021 "2022-06-29T14:31:18Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:32065116"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4030021 "connecting tubule B-IC"^^xsd:string) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9890303"^^xsd:string) oboInOwl:hasExactSynonym obo:CL_4030021 "kidney connecting tubule intercalated cell type B"^^xsd:string) @@ -28881,7 +28882,7 @@ EquivalentClasses(obo:CL_4030021 ObjectIntersectionOf(obo:CL_0002201 ObjectSomeV # Class: obo:CL_4030022 (renal medullary fibroblast) AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "PMID:10559635"^^xsd:string) obo:IAO_0000115 obo:CL_4030022 "A fibroblast that is located in the renal medulla interstitium."^^xsd:string) -AnnotationAssertion( obo:CL_4030022 ) +AnnotationAssertion( obo:CL_4030022 ) AnnotationAssertion( obo:CL_4030022 "2022-07-05T12:13:40Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030022 "kidney medullary fibroblast"^^xsd:string) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10559635"^^xsd:string) rdfs:comment obo:CL_4030022 "It has been noted that inner medullary fibroblasts are involved in the regulation of water and electrolyte homeostasis."^^xsd:string) @@ -28891,7 +28892,7 @@ EquivalentClasses(obo:CL_4030022 ObjectIntersectionOf(obo:CL_0000057 ObjectSomeV # Class: obo:CL_4030023 (respiratory hillock cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref ) Annotation(oboInOwl:hasDbXref "PMID:30069044"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:32726565"^^xsd:string) Annotation(oboInOwl:hasDbXref "PMID:33442032"^^xsd:string) obo:IAO_0000115 obo:CL_4030023 "A hillock cell that is located in respiratory epithelium. In some mammalian species, this cell type has been noted to express KRT13 and KRT4 and is postulated to play a role in squamous barrier function and immunomodulation."^^xsd:string) -AnnotationAssertion( obo:CL_4030023 ) +AnnotationAssertion( obo:CL_4030023 ) AnnotationAssertion( obo:CL_4030023 "2022-06-06T08:31:09Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasNarrowSynonym obo:CL_4030023 "hillock cell of respiratory tract"^^xsd:string) AnnotationAssertion(rdfs:label obo:CL_4030023 "respiratory hillock cell"^^xsd:string) @@ -28901,7 +28902,7 @@ SubClassOf(obo:CL_4030023 obo:CL_0002368) # Class: obo:CL_4030024 (hillock cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:30069044"^^xsd:string) obo:IAO_0000115 obo:CL_4030024 "An epithelial, transitional cell type between basal and secretory; located in stratified, non-ciliated structures (called hillocks) with high cell turnover in epithelium. In some mammalian species, this cell type has been noted to express KRT13 and is postulated to play a role in squamous barrier function and immunomodulation."^^xsd:string) -AnnotationAssertion( obo:CL_4030024 ) +AnnotationAssertion( obo:CL_4030024 ) AnnotationAssertion( obo:CL_4030024 "2022-06-24T14:52:24Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label obo:CL_4030024 "hillock cell") SubClassOf(obo:CL_4030024 obo:CL_0000066) @@ -28909,7 +28910,7 @@ SubClassOf(obo:CL_4030024 obo:CL_0000066) # Class: obo:CL_4030025 (renal cortical fibroblast) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10559635"^^xsd:string) obo:IAO_0000115 obo:CL_4030025 "A fibroblast that is located in the renal cortical interstitium."^^xsd:string) -AnnotationAssertion( obo:CL_4030025 ) +AnnotationAssertion( obo:CL_4030025 ) AnnotationAssertion( obo:CL_4030025 "2022-07-05T15:50:17Z"^^xsd:dateTime) AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4030025 "kidney cortical fibroblast"^^xsd:string) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:16230044"^^xsd:string) rdfs:comment obo:CL_4030025 "Renal cortical fibroblasts have key roles in mediating intercellular communication with neighboring/infiltrating cells and extracellular matrix and maintenance of renal tissue architecture. They additionally have an endocrine function in the production of epoetin."^^xsd:string) diff --git a/src/sparql/illegal-annotation-property-violation.sparql b/src/sparql/illegal-annotation-property-violation.sparql index 2ebd81e59..d8ebff406 100644 --- a/src/sparql/illegal-annotation-property-violation.sparql +++ b/src/sparql/illegal-annotation-property-violation.sparql @@ -1,7 +1,7 @@ PREFIX owl: -SELECT DISTINCT ?annotation WHERE { +SELECT DISTINCT ?term ?annotation WHERE { ?annotation a owl:AnnotationProperty . - ?subj ?annotation ?o . + ?term ?annotation ?o . FILTER (?annotation NOT IN ( , , @@ -51,5 +51,5 @@ SELECT DISTINCT ?annotation WHERE { , )) - FILTER (isIRI(?subj) && STRSTARTS(str(?subj), "http://purl.obolibrary.org/obo/CL_")) + FILTER (isIRI(?term) && STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/CL_")) }