Issues

• OLS embeddings: API ergonomics (obsolete terms in results, 500 for non-embeddable model, no bulk access)

  INCATools/ontology-access-kit#918 · Filter by author cmungall opened on Oct 5, 2026

• OLS embeddings: text search (llm_search) misses exact label matches

  INCATools/ontology-access-kit#917 · Filter by author cmungall opened on Oct 5, 2026

• OLS embeddings: vector search scores disagree with the served vectors (self-match < 1, ties)

  INCATools/ontology-access-kit#916 · Filter by author cmungall opened on Oct 5, 2026

• OLS embeddings: similarity scores are (1 + cosine) / 2, not cosine (undocumented)

  INCATools/ontology-access-kit#915 · Filter by author cmungall opened on Oct 5, 2026

• precompute_lookups() costs 2.62 GB on NCBITaxon with no docstring or indication that cost scales with ontology size

  INCATools/ontology-access-kit#910 · Filter by author turbomam opened on Sep 10, 2026

• Several methods return set-derived lists, so their order changes between processes

  INCATools/ontology-access-kit#909 · Filter by author turbomam opened on Sep 9, 2026

• Remove upper version pin for python from OAK

  INCATools/ontology-access-kit#905 · Filter by author matentzn opened on Jul 15, 2026
  2

• Unify the versions of all actions and updating them to latest

  INCATools/ontology-access-kit#904 · Filter by author matentzn opened on Jul 15, 2026

• tests/test_implementations/test_bioportal.py is fragile

  INCATools/ontology-access-kit#903 · Filter by author DnlRKorn opened on Jul 15, 2026
  3

• Add Python 3.14 to the compatibility matrix

  INCATools/ontology-access-kit#901 · Filter by author matentzn opened on Jul 14, 2026
  3

• Epic: reduce dependencies on central sqlite database

  INCATools/ontology-access-kit#889 · Filter by author cmungall opened on Jul 2, 2026

• Ubergraph descendants() treats bare string CURIE input as characters

  INCATools/ontology-access-kit#887 · Filter by author cmungall opened on Jun 20, 2026

• OLS adapter graph traversal lacks descendants() and reflexive keyword parity

  INCATools/ontology-access-kit#886 · Filter by author cmungall opened on Jun 20, 2026

• OLS adapter label() returns None for OLS4 term payloads

  INCATools/ontology-access-kit#885 · Filter by author cmungall opened on Jun 20, 2026

• Slow "naive approach" root detection: no adapter overrides the base impl, hits noticeably at 2.7M-node scale

  INCATools/ontology-access-kit#881 · Filter by author turbomam opened on May 20, 2026
  2

• Reduce S3 egress costs for bbop-sqlite database downloads

  INCATools/ontology-access-kit#880 · Filter by author cmungall opened on May 11, 2026

• axioms of info output have wrong labels

  INCATools/ontology-access-kit#877 · Filter by author voxspox opened on May 8, 2026

• Optimize horned-owl text search for large local OWL ontologies

  INCATools/ontology-access-kit#871 · Filter by author cmungall opened on Apr 7, 2026

• oaklib fails to import with linkml-runtime 1.10.0: Format.JSON removed

  INCATools/ontology-access-kit#867 · Filter by author cmungall opened on Apr 1, 2026
  1

• feature request: enhance term enrichment figures

  INCATools/ontology-access-kit#866 · Filter by author wdduncan opened on Mar 24, 2026
  1

• broken link in enrichment demo

  INCATools/ontology-access-kit#865 · Filter by author wdduncan opened on Mar 23, 2026

• HPOA parser does not account for negation qualifier

  INCATools/ontology-access-kit#862 · Filter by author bpow opened on Feb 26, 2026

• Chore: Getting SADeprecationWarning in SQL code

  INCATools/ontology-access-kit#861 · Filter by author DnlRKorn opened on Feb 24, 2026
  1

• Chore: Curies currently needs to be locked to version 11

  chore
  INCATools/ontology-access-kit#855 · Filter by author DnlRKorn opened on Feb 20, 2026
  1

  

• Chore: Gilda annotate changes return data format in release 1.5.0

  INCATools/ontology-access-kit#854 · Filter by author DnlRKorn opened on Feb 20, 2026