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Cleanup untracked scratch on kg-microbe main tree

Status: Open.

#579 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on Jul 2, 2026

metpo-proposal: route reused-ontology CURIEs to mappings, not definition_source

Status: Open.

#572 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on May 29, 2026

explore nmdc.cn data

Status: Open.

#569 In Knowledge-Graph-Hub/kg-microbe;

· realmarcin opened on May 19, 2026

mapping_file_utils.load_metpo_mappings reads non-existent 'biolink equivalent' column from METPO sheet

Status: Open.

#568 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on May 18, 2026

Deprecated biolink:ChemicalSubstance still used in custom_curies.yaml and merged graph

Status: Open.

#557 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on Apr 24, 2026

Tracking: kg-microbe governance & cleanup backlog from 2026-04-17 audit

Status: Open.

#555 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on Apr 20, 2026

Release asset contents and download paths are undocumented

Status: Open.

#553 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on Apr 17, 2026

master fails ruff check on 3.12 CI — 7 lint errors in tests/test_mediadive_bulk_download.py

Status: Open.

#549 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on Apr 17, 2026

KGX transform produces URIs with unencoded characters (:, >, °, etc.) that break downstream NT serialization

Status: Open.

#547 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on Apr 17, 2026

Security & governance baseline: 30 Dependabot alerts, no branch protection, missing standard configs

Status: Open.

#546 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on Apr 17, 2026

.gitignore: data/transformed/bacdive/ and madin_etal/ aren't ignored, but cog/ and bactotraits/ are

Status: Open.

#545 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on Apr 17, 2026

BacDive transformer opens ncbitaxon.owl with a sqlite adapter (path/format mismatch)

Status: Open.

#544 In Knowledge-Graph-Hub/kg-microbe;

· turbomam opened on Apr 17, 2026