Issues

• docs/NEXT_TASKS.md lists closed blockers and a host-local worktree, and its acceptance review does not require full coverage

  Knowledge-Graph-Hub/kg-microbe#1675 · Filter by author realmarcin opened on Oct 16, 2026

• Canonicalize single-valued node columns, deduplicate repeated descriptions, and ignore blank names at merge

  Knowledge-Graph-Hub/kg-microbe#1674 · Filter by author realmarcin opened on Oct 16, 2026

• semsql make exits 0 when make fails; a failed build is reported only by validation

  Knowledge-Graph-Hub/kg-microbe#1664 · Filter by author realmarcin opened on Oct 14, 2026
  1

• Phased HPC transform: a failed source cancels later phases even for sources that do not read it

  Knowledge-Graph-Hub/kg-microbe#1659 · Filter by author realmarcin opened on Oct 14, 2026

• Nodes with different SemSQL toolchains sharing one data/raw rebuild go.db in turn

  Knowledge-Graph-Hub/kg-microbe#1643 · Filter by author realmarcin opened on Oct 14, 2026

• ontologies_stubs freshness does not cover bto.db or the pinned import modules

  Knowledge-Graph-Hub/kg-microbe#1503 · Filter by author realmarcin opened on Oct 12, 2026

• [Review #1467] Records with only a late, name-derived parent never contest a deposit

  bug
  Knowledge-Graph-Hub/kg-microbe#1486 · Filter by author realmarcin opened on Oct 12, 2026

• [Review #1467] Recorded replay does not verify close_match suppression or the deposit-claims report

  bug
  Knowledge-Graph-Hub/kg-microbe#1483 · Filter by author realmarcin opened on Oct 12, 2026

• Bakta per-dataset outputs are not tied to the run that wrote the fingerprint, so a stale dataset can be merged

  Knowledge-Graph-Hub/kg-microbe#1458 · Filter by author realmarcin opened on Oct 12, 2026

• [Review #1442] KEGG fails the default transform batch when its manually fetched KO cache is missing

  Knowledge-Graph-Hub/kg-microbe#1448 · Filter by author realmarcin opened on Oct 12, 2026

• [Review #1401] MetaTraits reads ec2go.txt, NCBI2GTDB.tsv.gz and metpo.json from the checkout's data/raw, ignoring --input-dir

  bug
  Knowledge-Graph-Hub/kg-microbe#1437 · Filter by author realmarcin opened on Oct 11, 2026
  1

• [Review #1401] CI sets KG_MICROBE_TESTS_NO_NETWORK but no code reads it and tox does not pass it through

  bug
  Knowledge-Graph-Hub/kg-microbe#1436 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] BacDive ancestry authority finish() re-hashes the whole shared admission, including the 14 GB ncbitaxon.db

  enhancement
  Knowledge-Graph-Hub/kg-microbe#1435 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] Reviewed supplied-taxid withholding lapses when a record's priority level changes

  bug
  Knowledge-Graph-Hub/kg-microbe#1434 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] Switch MicrobeDecoder genome crosswalks (ncbi.assembly and IMG) from close_match to biolink:in_taxon

  bug
  Knowledge-Graph-Hub/kg-microbe#1433 · Filter by author realmarcin opened on Oct 11, 2026
  1

• [Review #1401] MicrobeDecoder emits close_match to GOLD organism IDs the GOLD producer did not admit

  bug
  Knowledge-Graph-Hub/kg-microbe#1432 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] Category authority decisions are not reconciled with other producers' substantive categories

  bug
  Knowledge-Graph-Hub/kg-microbe#1431 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] foodon_category() still defaults to data/raw/foodon.json with a silent fallback

  bug
  Knowledge-Graph-Hub/kg-microbe#1430 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] MICRO culture media typed only as biolink:GrowthMedium without the documented mixture category

  bug
  Knowledge-Graph-Hub/kg-microbe#1429 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] Abiotic ENVO features typed AnatomicalEntity through ENVO's UBERON anatomy is_a

  bug
  Knowledge-Graph-Hub/kg-microbe#1428 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] Generic category authority types PO whole-plant descendants (pollen, embryo, seedling) as OrganismTaxon

  bug
  Knowledge-Graph-Hub/kg-microbe#1427 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] GOLD reference-request rescans run for every source at finalization and merge admission

  enhancement
  Knowledge-Graph-Hub/kg-microbe#1426 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] PREGO dictionary synonyms reuse size/mtime-keyed caches outside the native-input contract

  bug
  Knowledge-Graph-Hub/kg-microbe#1425 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] Committed unified SSSOM not regenerated under the ingredient-context policy

  bug
  Knowledge-Graph-Hub/kg-microbe#1424 · Filter by author realmarcin opened on Oct 11, 2026

• [Review #1401] PREGO payload binding copies and re-hashes about 14 GB per run and again at merge

  enhancement
  Knowledge-Graph-Hub/kg-microbe#1423 · Filter by author realmarcin opened on Oct 11, 2026
  1