Feature/sparql qc queries

[shanmukhkalasamudram]

Query	Checks
CCO_classes_have_BFO_superclass	Fixed — old namespace was dead, always passed silently
no_cco_elucidation	No terms using deprecated v1 elucidation property
missing_definition_source	All terms have a definition source annotation
exactly_1_label	Every term has exactly one rdfs:label
exactly_1_curated_in	Every term has exactly one "curated in ontology" annotation
annotation_language_tag	All natural-language annotations carry @en tag
iri_format_check	All IRIs match ont + 8-digit format
curated_in_matches_ontology	"Curated in" values point to a valid CCO module IRI
no_duplicate_declarations	No term declared as two different OWL types
duplicate_iri_number	No two terms share the same 8-digit numeric fragment across namespaces

[johnbeve]

@shanmukhkalasamudram Did you check that these return the expected results? If so, can you provide the results of your testing in the comments here?

[shanmukhkalasamudram]

Hi @johnbeve — yes, tested locally by running all 19 SPARQL queries via robot verify against the merged ontology (ccom-raw.ttl). Results below.

Impact summary: After this PR, every push runs 19 checks. Seven pass completely clean against the current ontology, giving us a reliable release gate for those properties. The remaining queries surfaced pre-existing issues that were previously invisible — none were introduced by this PR.

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Queries passing clean (0 violations)

deprecated_property_reference · duplicate_definition · duplicate_iri_number · duplicate_label · exactly_1_prefLabel_per_lang · min_1_ontology_title · subclass_circularity

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Pre-existing issues surfaced by the new queries

Query	Findings	Severity
missing_definition_source	835 terms have a definition but no source citation	WARNING
min_1_eng_def	87 terms missing any English definition	WARNING
annotation_language_tag	12 annotations on 5 terms missing @en tag	ERROR
annotation_whitespace	8 annotation values with leading/trailing whitespace	ERROR
no_multiple_inverse_properties	ont00001995 has two owl:inverseOf declarations	ERROR
exactly_1_curated_in	ont00001660 (International Geomagnetic Reference Field) missing cco:ont00001760	ERROR

The remaining results contain only test-fixture IRIs (ont9999xxx) planted to verify detection logic — no real ontology terms appear in those results.

[shanmukhkalasamudram]

Full CSV results are attached as ontology_release_results in this CI run (completed successfully).