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Add sparql check for annotations #1659

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Jul 15, 2022
Merged

Add sparql check for annotations #1659

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665503a
add sparql check for annotations
Jul 14, 2022
4c685c6
replace dce to dcterms & add skos annotations
Jul 15, 2022
dae9759
replace `dc:date` to `dcterms:date`
Jul 15, 2022
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2 changes: 1 addition & 1 deletion src/ontology/Makefile
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Expand Up @@ -38,7 +38,7 @@ 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 orcid-contributor
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by orcid-contributor illegal-annotation-property
SPARQL_EXPORTS = basic-report
ODK_VERSION_MAKEFILE = v1.3.1

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1 change: 1 addition & 0 deletions src/ontology/cl-odk.yaml
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Expand Up @@ -82,6 +82,7 @@ robot_report:
- pmid-not-dbxref
- obsolete-replaced_by
- orcid-contributor
- illegal-annotation-property
custom_sparql_exports :
- basic-report
components:
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51 changes: 51 additions & 0 deletions src/sparql/illegal-annotation-property-violation.sparql
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@@ -0,0 +1,51 @@
PREFIX owl: <http://www.w3.org/2002/07/owl#>
SELECT DISTINCT ?annotation WHERE {
?annotation a owl:AnnotationProperty .
?subj ?annotation ?o .
FILTER (?annotation NOT IN (
<http://purl.obolibrary.org/obo/IAO_0000115>,
<http://purl.obolibrary.org/obo/IAO_0000116>,
<http://purl.obolibrary.org/obo/IAO_0000231>,
<http://purl.obolibrary.org/obo/IAO_0000232>,
<http://purl.obolibrary.org/obo/IAO_0000412>,
<http://purl.obolibrary.org/obo/IAO_0000589>,
<http://purl.obolibrary.org/obo/IAO_0100001>,
<http://purl.obolibrary.org/obo/RO_0002161>,
<http://purl.obolibrary.org/obo/RO_0002171>,
<http://purl.obolibrary.org/obo/RO_0002173>,
<http://purl.obolibrary.org/obo/RO_0002174>,
<http://purl.obolibrary.org/obo/RO_0002175>,
<http://purl.obolibrary.org/obo/RO_0002423>,
<http://purl.obolibrary.org/obo/RO_0002475>,
<http://purl.obolibrary.org/obo/RO_0002575>,
<http://purl.obolibrary.org/obo/RO_0002579>,
<http://purl.obolibrary.org/obo/RO_0002604>,
<http://purl.obolibrary.org/obo/RO_0004049>,
<http://purl.obolibrary.org/obo/RO_0004050>,
<http://purl.obolibrary.org/obo/RO_0040042>,
<http://purl.obolibrary.org/obo/term_editor>,
<http://purl.org/dc/terms/date>,
<http://purl.org/dc/elements/1.1/description>,
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dce should not be needed.

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wherever its used, change to dct

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Even in the ontology? It's not included here.

<http://purl.org/dc/terms/source>,
<http://purl.org/dc/terms/contributor>,
<http://purl.org/spar/cito/citesAsAuthority>,
<http://www.geneontology.org/formats/oboInOwl#consider>,
<http://www.geneontology.org/formats/oboInOwl#creation_date>,
<http://www.geneontology.org/formats/oboInOwl#hasAlternativeId>,
<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>,
<http://www.geneontology.org/formats/oboInOwl#hasDbXref>,
<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>,
<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym>,
<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace>,
<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>,
<http://www.geneontology.org/formats/oboInOwl#id>,
<http://www.geneontology.org/formats/oboInOwl#inSubset>,
<http://www.w3.org/2000/01/rdf-schema#comment>,
<http://www.w3.org/2000/01/rdf-schema#label>,
<http://www.w3.org/2000/01/rdf-schema#seeAlso>,
<http://www.w3.org/2004/02/skos/core#closeMatch>,
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<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_"))
}