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Backfill related_ingredients in 7 more communities (#30)#152

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realmarcin merged 1 commit into
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backfill/related-ingredients-batch8i
Jun 15, 2026
Merged

Backfill related_ingredients in 7 more communities (#30)#152
realmarcin merged 1 commit into
mainfrom
backfill/related-ingredients-batch8i

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Continues the #30 backfill — 30 CHEBI-grounded ingredients across 7 communities, strict no-fabrication protocol.

File #
PET_Artificial_FourSpecies_Degradation_Consortium 5
SMutans_CAlbicans_ECC_Biofilm 3
NCycle_Bioflocculation_Model_Consortium 1
Industrial_Bioreactor_Consortium 7
Rifle_Aquifer_Bioanode_EET_Community 2
Episymbiotic_CPR_DPANN_Groundwater_Community 2
East_River_Hillslope_Riparian_Transect_Community 10

Note: Industrial_Bioreactor turned out to be a bioleaching consortium (not anaerobic digestion) — captured Cu/Fe/S/chalcopyrite/pyrite chemistry accordingly. Model_Cyanobacterial_Consortia was attempted but its generic survey abstract named no compounds (correctly skipped, no fabrication).

Verification

  • 30/30 labels OAK-canonical; 30/30 snippets exact substrings
  • linkml-validate all 7 → exit 0
  • just validate-products (blocking gate) → exit 0 (5440 OK_CANONICAL, 184 OK_EXCEPTION, 0 errors)

Adoption: 197 → 204 / 265.

🤖 Generated with Claude Code

Adds 30 CHEBI-grounded related_ingredients across 7 communities, strict
no-fabrication protocol (OAK-verified canonical CHEBI labels; every snippet a
verbatim substring of a reference already cited + cached in the file).

- PET_Artificial_FourSpecies_Degradation_Consortium: 5 (PET, MHET, terephthalic
  acid, ethylene glycol, BHET)
- SMutans_CAlbicans_ECC_Biofilm: 3 (exopolysaccharide, (1->3)-beta-D-glucan, mannan)
- NCycle_Bioflocculation_Model_Consortium: 1 (alginate)
- Industrial_Bioreactor_Consortium: 7 (bioleaching — iron(2+) sulfate, sulfur,
  chalcopyrite, copper(2+), iron(3+), CO2, pyrite)
- Rifle_Aquifer_Bioanode_EET_Community: 2 (acetate, iron oxide)
- Episymbiotic_CPR_DPANN_Groundwater_Community: 2 (glucose, pyruvate)
- East_River_Hillslope_Riparian_Transect_Community: 10 (N/S/Se species, methane,
  methanol, CO)

(Model_Cyanobacterial_Consortia_Core_Microbiome attempted but skipped — generic
survey abstract names no compounds; no fabrication.)

Verified: 30/30 labels canonical, 30/30 snippets exact, all 7 pass
linkml-validate, and `just validate-products` (blocking gate) exits 0.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
@realmarcin realmarcin merged commit 02eb2e4 into main Jun 15, 2026
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@realmarcin realmarcin deleted the backfill/related-ingredients-batch8i branch June 15, 2026 07:14
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