Issues

• efetch by SAMD or SAMEA accession returns the wrong BioSample

  microbiomedata/external-metadata-awareness#592 · Filter by author turbomam opened on Oct 16, 2026

• Docs still describe the GOLD and NMDC pipelines removed in May 2026 as runnable

  microbiomedata/external-metadata-awareness#584 · Filter by author turbomam opened on Oct 13, 2026

• Read inflow and effluent from BioSample sample names, then train a wastewater subtype classifier

  enhancement
  microbiomedata/external-metadata-awareness#580 · Filter by author turbomam opened on Oct 13, 2026
  3

• Find wastewater biosamples without relying on the NCBI package

  microbiomedata/external-metadata-awareness#570 · Filter by author turbomam opened on Sep 22, 2026
  4

• [bot] semsql pulls reference the retiring raw bbop-sqlite bucket (URL swap + one ListBucket dependency)

  microbiomedata/external-metadata-awareness#553 · Filter by author kltm opened on Aug 18, 2026
  1

• Record structured NCBI Parquet export measurements

  microbiomedata/external-metadata-awareness#552 · Filter by author turbomam opened on Aug 18, 2026

• Stage NCBI Parquet products before safe promotion

  microbiomedata/external-metadata-awareness#551 · Filter by author turbomam opened on Aug 18, 2026

• Publish validated manifests for NCBI Parquet export bundles

  microbiomedata/external-metadata-awareness#550 · Filter by author turbomam opened on Aug 18, 2026

• Docs still reference flatten_nmdc_collections.py, removed in PR 422

  microbiomedata/external-metadata-awareness#546 · Filter by author turbomam opened on Aug 11, 2026

• Credentials with reserved characters are not percent-encoded when injected into the Mongo URI

  microbiomedata/external-metadata-awareness#530 · Filter by author turbomam opened on Jul 27, 2026
  1

• MIxS required-slot gap report: which checklist/extension slots lack an NMDC home, weighted by submission-portal usage

  microbiomedata/external-metadata-awareness#491 · Filter by author turbomam opened on Jun 23, 2026

• Extract pure env-triad parsing helpers into a stdlib-only module

  microbiomedata/external-metadata-awareness#481 · Filter by author turbomam opened on Jun 17, 2026

• Repo bloat: stop committing generated outputs/logs; trim large tracked files

  microbiomedata/external-metadata-awareness#478 · Filter by author turbomam opened on Jun 17, 2026

• Add a smoke-test layer to catch dependency and refactor breakage

  microbiomedata/external-metadata-awareness#470 · Filter by author turbomam opened on Jun 16, 2026
  1

• Evaluate pandas 3.x migration

  backlog
  microbiomedata/external-metadata-awareness#469 · Filter by author turbomam opened on Jun 16, 2026
  2

• Adopt .env-file-as-canonical-per-env-config pattern in other Makefiles

  microbiomedata/external-metadata-awareness#441 · Filter by author turbomam opened on May 28, 2026

• Document M5 Keychain credential pattern for authed local MongoDB

  microbiomedata/external-metadata-awareness#440 · Filter by author turbomam opened on May 28, 2026

• Unify MongoDB connection config across EMA pipelines

  microbiomedata/external-metadata-awareness#439 · Filter by author turbomam opened on May 28, 2026
  1

• Framework to anticipate/discover/hypothesis-test noise patterns in biosample free-text fields

  microbiomedata/external-metadata-awareness#428 · Filter by author turbomam opened on May 19, 2026

• Extend deterministic ontology normalization beyond env_triad (isolation_source, host, geo_loc_name, Description.Title)

  microbiomedata/external-metadata-awareness#427 · Filter by author turbomam opened on May 19, 2026

• Deterministic env-triad CURIE lookup table that agents query before LLM resolution

  microbiomedata/external-metadata-awareness#426 · Filter by author turbomam opened on May 19, 2026

• Drop normalize-satisfying-biosamples (CSV-writing) when implementing #424

  microbiomedata/external-metadata-awareness#425 · Filter by author turbomam opened on May 19, 2026

• Single Makefile target to load, flatten, and count NCBI/SRA MongoDB collections (no external APIs, no entity recognition)

  microbiomedata/external-metadata-awareness#424 · Filter by author turbomam opened on May 19, 2026

• sra_metadata.Makefile MONGO_URI redefinition silently no-ops when invoked via root Makefile

  microbiomedata/external-metadata-awareness#415 · Filter by author turbomam opened on May 18, 2026

• Footgun: MONGO_USER vs MONGO_USERNAME silently splits which scripts can authenticate

  microbiomedata/external-metadata-awareness#412 · Filter by author turbomam opened on May 18, 2026
  1