Skip to content

Commit

Permalink
Fix contributor QC (#1734)
Browse files Browse the repository at this point in the history 
* add annotation declaration dce:contributor and run normalize_src

* normalise xsd string

Co-authored-by: Anita Caron <[email protected]>
  • Loading branch information
@anitacaron
Anita Caron and anitacaron authored Nov 22, 2022
1 parent fdec2a9 commit 8a66eea
Show file tree
Hide file tree
Showing 2 changed files with 17 additions and 16 deletions.
27 changes: 14 additions & 13 deletions src/ontology/cl-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2882,6 +2882,7 @@ Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon#LATIN>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon#PLURAL>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ubprop#_upper_level>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/contributor>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/description>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/license>))
Declaration(AnnotationProperty(<http://purl.org/dc/elements/1.1/title>))
Expand Down Expand Up @@ -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(<http://purl.org/dc/elements/1.1/contributor> <http://orcid.org/000-0003-1940-6740>) Annotation(oboInOwl:hasDbXref <https://doi.org/10.1038/s12276-020-0483-0>) oboInOwl:hasExactSynonym obo:CL_0002196 "hepatic progenitor cell"^^xsd:string)
AnnotationAssertion(Annotation(<http://purl.org/dc/terms/contributor> <http://orcid.org/0000-0003-1940-6740>) Annotation(oboInOwl:hasDbXref <https://doi.org/10.1038/s12276-020-0483-0>) oboInOwl:hasExactSynonym obo:CL_0002196 "hepatic progenitor cell"^^xsd:string)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://doi.org/10.1038/s12276-020-0483-0>) 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)
Expand Down Expand Up @@ -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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_0700009 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_0700009 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)
Expand Down Expand Up @@ -28676,7 +28677,7 @@ SubClassOf(obo:CL_4030000 obo:CL_0000148)
# Class: obo:CL_4030001 (stromal cell of thymus)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://www.nature.com/articles/s41467-020-20082-7>) obo:IAO_0000115 obo:CL_4030001 "A stromal cell that is part of the thymus."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030001 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030001 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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")
Expand All @@ -28698,7 +28699,7 @@ SubClassOf(obo:CL_4030002 obo:CL_0000791)
# Class: obo:CL_4030003 (interstitial cell of thymus)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://www.nature.com/articles/s41467-020-20082-7>) obo:IAO_0000115 obo:CL_4030003 "A cell that makes up the loose connective tissue of the thymus."^^xsd:string)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030003 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030003 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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")
Expand All @@ -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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030005 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030005 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)
Expand Down Expand Up @@ -28844,15 +28845,15 @@ EquivalentClasses(obo:CL_4030017 ObjectIntersectionOf(obo:CL_0000066 ObjectSomeV
# Class: obo:CL_4030018 (kidney connecting tubule principal cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref <http://orcid.org/0000-0003-2804-127X>) 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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030018 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030018 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)))

# 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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030019 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030019 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)))
Expand All @@ -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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030020 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030020 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)
Expand All @@ -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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030021 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030021 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)
Expand All @@ -28881,7 +28882,7 @@ EquivalentClasses(obo:CL_4030021 ObjectIntersectionOf(obo:CL_0002201 ObjectSomeV
# Class: obo:CL_4030022 (renal medullary fibroblast)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://doi.org/10.1101/2021.07.28.454201>) 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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030022 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030022 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)
Expand All @@ -28891,7 +28892,7 @@ EquivalentClasses(obo:CL_4030022 ObjectIntersectionOf(obo:CL_0000057 ObjectSomeV
# Class: obo:CL_4030023 (respiratory hillock cell)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref <https://orcid.org/0000-0001-7772-9578>) 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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030023 <http://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030023 <http://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)
Expand All @@ -28901,15 +28902,15 @@ 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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030024 <http://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030024 <http://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)

# 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(<http://purl.org/dc/elements/1.1/contributor> obo:CL_4030025 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/contributor> obo:CL_4030025 <https://orcid.org/0000-0002-1773-2692>)
AnnotationAssertion(<http://purl.org/dc/terms/date> 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)
Expand Down
6 changes: 3 additions & 3 deletions src/sparql/illegal-annotation-property-violation.sparql
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?annotation WHERE {
SELECT DISTINCT ?term ?annotation WHERE {
?annotation a owl:AnnotationProperty .
?subj ?annotation ?o .
?term ?annotation ?o .
FILTER (?annotation NOT IN (
<http://purl.obolibrary.org/obo/IAO_0000115>,
<http://purl.obolibrary.org/obo/IAO_0000116>,
Expand Down Expand Up @@ -51,5 +51,5 @@ SELECT DISTINCT ?annotation WHERE {
<http://www.w3.org/2002/07/owl#deprecated>,
<http://xmlns.com/foaf/0.1/depicted_by>
))
FILTER (isIRI(?subj) && STRSTARTS(str(?subj), "http://purl.obolibrary.org/obo/CL_"))
FILTER (isIRI(?term) && STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/CL_"))
}

0 comments on commit 8a66eea

Please sign in to comment.