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Add check for definition xrefs that are not also term xrefs #29161

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Add check for definition xrefs that are not also term xrefs #29161

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ffda910
Add check for definition xrefs that are not also term xrefs.
balhoff Nov 6, 2024
50cf658
Exclude obsolete terms.
balhoff Nov 6, 2024
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2 changes: 1 addition & 1 deletion src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -643,7 +643,7 @@ imports/go-taxon-groupings.obo: imports/go-taxon-groupings.owl
# these live in the ../sparql directory, and have suffix -violation.sparql
# adding the name here will make the violation check live

VCHECKS = equivalent-classes trailing-whitespace owldef-self-reference synonym-label-match replacedby-obsolete replacedby-namespace duplicate-exact-synonym duplicate-synonym non-IRI-value non-anyURI-value obsolete-definition definition-constraints one-to-one-xrefs-by-subject one-to-one-xrefs-by-value xref-syntax
VCHECKS = equivalent-classes trailing-whitespace owldef-self-reference synonym-label-match replacedby-obsolete replacedby-namespace duplicate-exact-synonym duplicate-synonym non-IRI-value non-anyURI-value obsolete-definition definition-constraints one-to-one-xrefs-by-subject one-to-one-xrefs-by-value xref-syntax missing-defxref-as-xref

# run all violation checks
VARGS = $(foreach V,$(VCHECKS), $(SPARQLDIR)/$V-violation.sparql)
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27 changes: 27 additions & 0 deletions src/sparql/missing-defxref-as-xref-violation.sparql
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@@ -0,0 +1,27 @@
prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
prefix definition: <http://purl.obolibrary.org/obo/IAO_0000115>
prefix owl: <http://www.w3.org/2002/07/owl#>

SELECT DISTINCT ?cls ?defxref
WHERE
{
?cls a owl:Class .
FILTER NOT EXISTS {
?cls owl:deprecated true .
}
[
a owl:Axiom ;
owl:annotatedSource ?cls ;
owl:annotatedProperty definition: ;
oio:hasDbXref ?defxref
]
FILTER(STRSTARTS(?defxref, "RHEA")
|| STRSTARTS(?defxref, "EC")
|| STRSTARTS(?defxref, "MetaCyc")
|| STRSTARTS(?defxref, "KEGG")
|| STRSTARTS(?defxref, "UM-BBD")
|| STRSTARTS(?defxref, "TC"))
FILTER NOT EXISTS {
?cls oio:hasDbXref ?defxref .
}
}
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