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add def-not-only-xref-violation.sparql (#2549)
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This violation has results when a definition has other annotations
than `oio:hasDbXref`. Only `oio:hasDbXref` is allowed in the definition.

Co-authored-by: Anita Caron <[email protected]>
Co-authored-by: CEastwood <[email protected]>
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3 people authored Sep 12, 2024
1 parent 300ce8a commit 29b9465
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Showing 3 changed files with 21 additions and 2 deletions.
4 changes: 2 additions & 2 deletions src/ontology/Makefile
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Expand Up @@ -10,7 +10,7 @@
# More information: https://github.com/INCATools/ontology-development-kit/

# Fingerprint of the configuration file when this Makefile was last generated
CONFIG_HASH= b30da9471aba970de63ae9153976cf8ce20f44a23d2dda7923dc04560cd0ae11
CONFIG_HASH= 5726a8effc41f60465bcbc0d3b62fc006af7e9379ed79932a5b119ca0ad5039f


# ----------------------------------------
Expand Down Expand Up @@ -44,7 +44,7 @@ REPORT_FAIL_ON = ERROR
REPORT_LABEL =
REPORT_PROFILE_OPTS =
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy illegal-date
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy illegal-date def-not-only-xref
SPARQL_EXPORTS = cl_terms cl-edges cl-synonyms cl-xrefs cl-def-xrefs
ODK_VERSION_MAKEFILE = v1.5.2

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1 change: 1 addition & 0 deletions src/ontology/cl-odk.yaml
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Expand Up @@ -116,6 +116,7 @@ robot_report:
- illegal-annotation-property
- label-synonym-polysemy
- illegal-date
- def-not-only-xref
custom_sparql_exports:
- cl_terms
- cl-edges
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18 changes: 18 additions & 0 deletions src/sparql/def-not-only-xref-violation.sparql
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@@ -0,0 +1,18 @@
PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX definition: <http://purl.obolibrary.org/obo/IAO_0000115>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT ?cls ?annotation WHERE
{
?cls definition: ?def .
?ax a owl:Axiom;
owl:annotatedSource ?cls;
owl:annotatedProperty definition:;
owl:annotatedTarget ?def;
?annotation ?value .
FILTER NOT EXISTS { ?cls owl:deprecated "true"^^xsd:boolean . }
FILTER(isIRI(?cls) && STRSTARTS(str(?cls), "http://purl.obolibrary.org/obo/CL_") || STRSTARTS(str(?cls), "http://purl.obolibrary.org/obo/cl#"))
FILTER (?annotation NOT IN (rdf:type, owl:annotatedSource, owl:annotatedProperty, owl:annotatedTarget, oio:hasDbXref))
}

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