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Add QC checks for obsolete labels and phenotype root (#1011) #1021

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Add QC checks for obsolete labels and phenotype root (#1011) #1021

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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -323,3 +323,4 @@ src/ontology/reports/xrefs.tsv
src/ontology/imports/*.json
/src/metadata
src/mappings/*.owl
.claude/
2 changes: 1 addition & 1 deletion src/ontology/Makefile
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Expand Up @@ -47,7 +47,7 @@ REPORT_FAIL_ON = None
REPORT_LABEL =
REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE)
OBO_FORMAT_OPTIONS = --clean-obo "strict drop-untranslatable-axioms"
SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range
SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range upheno-label-obsolete upheno-no-phenotype-root
SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
ODK_VERSION_MAKEFILE = v1.6
RELAX_OPTIONS = --include-subclass-of true
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13 changes: 13 additions & 0 deletions src/sparql/upheno-label-obsolete-violation.sparql
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@@ -0,0 +1,13 @@
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT ?cls ?label WHERE {
?cls a owl:Class ;
rdfs:label ?label .
FILTER(STRSTARTS(STR(?cls), "http://purl.obolibrary.org/obo/UPHENO_"))
FILTER(CONTAINS(LCASE(?label), "obsolete"))
FILTER(NOT EXISTS { ?cls owl:deprecated "true"^^xsd:boolean })
}
ORDER BY ?cls
13 changes: 13 additions & 0 deletions src/sparql/upheno-no-phenotype-root-violation.sparql
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@@ -0,0 +1,13 @@
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT ?cls ?label WHERE {
?cls a owl:Class ;
rdfs:label ?label .
FILTER(STRSTARTS(STR(?cls), "http://purl.obolibrary.org/obo/UPHENO_"))
FILTER(NOT EXISTS { ?cls owl:deprecated "true"^^xsd:boolean })
FILTER(NOT EXISTS { ?cls rdfs:subClassOf* obo:UPHENO_0001001 })
}
ORDER BY ?cls