SNORQL audit: update SPARQL queries for owl:sameAs predicate migration

[marvinm2]

Summary

Phase 3 (predicate correction) changes the cross-database identifier predicate from skos:exactMatch to owl:sameAs in the generated RDF output. This issue documents the full audit of SPARQL queries that consume these predicates and tracks updates needed in both this repository and the external aopwiki-snorql-extended repository.

Audit Inventory

This repository (AOPWikiRDF) — UPDATED

All occurrences in this repo have been updated from skos:exactMatch to owl:sameAs.

SPARQLQueries/SPARQLqueries (6 occurrences — all updated)

Line	Query Context	Status
58	Genes mapped with PR — count HGNC IDs via protein ontology links	Updated
59	Genes mapped with PR — count Entrez Gene IDs	Updated
60	Genes mapped with PR — count Ensembl IDs	Updated
68	Gene IDs — count Entrez cross-references	Updated
69	Gene IDs — count RefSeq cross-references	Updated
70	Gene IDs — count Ensembl cross-references	Updated

SPARQLQueries/Federated queries (1 occurrence — updated)

Line	Query Context	Status
90	Federated query joining KE biological objects with UniProt via AOP DB	Updated

AOP-Wiki_stats.ipynb (3 occurrences — all updated)

Cell	Query Context	Status
26	Chemical identifier type enumeration	Updated
29	Key Event biological object type enumeration	Updated
30	Biological object entity count by type with labels	Updated

hgnc: symbol patterns

No hgnc:SYMBOL patterns found in any SPARQL query files or notebooks. No action needed for HGNC URI format changes in queries.

External: aopwiki-snorql-extended — NEEDS AUDIT

• Clone and grep aopwiki-snorql-extended for skos:exactMatch patterns
• Identify all affected queries
• Update queries to use owl:sameAs
• Verify queries work with dual-predicate output (both skos:exactMatch and owl:sameAs emitted during transition)
• Submit PR or update directly

Backward Compatibility

The RDF generation pipeline includes a dual-predicate transition flag (emit_legacy_predicates in PipelineConfig):

• When True (default): both skos:exactMatch AND owl:sameAs are emitted
• When False: only owl:sameAs is emitted

This ensures existing SPARQL consumers continue to work during the transition period. The flag should only be set to False after all downstream consumers have been updated.

Timeline

1. This repo queries: Updated (this commit)
2. External repo audit: To be completed before disabling legacy predicates
3. Disable legacy predicates: After all consumers confirmed updated