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references_cache commits publisher-copyrighted text to a public repo, with no licence record

Status: Open.

#754 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 10, 2026

SYNTROPHY is defined as "obligate" cooperation but is used for facultative pairings

Status: Open.

#752 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 8, 2026

biological_processes accepts any GO term: 30 entries are molecular functions or cellular components

Status: Open.

#751 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 8, 2026

No InteractionTypeEnum value fits cell fusion, cytoplasmic material exchange, or HGT

Status: Open.

#749 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 8, 2026

abundance_level's documented thresholds are impossible for most defined communities that use it

Status: Open.

#748 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 8, 2026

gtdb_ground.py default paths miss the KG-Hub kg-microbe layout, and strain-level ids no longer ground

Status: Open.

#746 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 8, 2026

The #740 relock downgraded biolink-model, curies, linkml and koza to satisfy an exact pin — not forced by oaklib, and an upward path exists

Status: Open.

#741 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 6, 2026

The schema-gap-analysis snapshot is stale in every one of its numbers

Status: Open.

#738 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 4, 2026

Two OAK cache key schemes that cannot share: label-correspondence restores 196 bytes while validate-strict has 3 GB

Status: Open.

#734 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 2, 2026

Both Engine A gates report SKIPPED, NOT PASSED on main — 20 GB of cache restored and no ontology reachable

Status: Open.

#732 In CultureBotAI/CommunityMech;

· realmarcin opened on Sep 2, 2026

KGX export: literal newlines in node descriptions make the TSV mean two things

Status: Open.

#723 In CultureBotAI/CommunityMech;

· realmarcin opened on Aug 31, 2026

Adopt the /source-queue skill and a licence-verified data-source queue

Status: Open.

#722 In CultureBotAI/CommunityMech;

· realmarcin opened on Aug 31, 2026