#30 backfill batch 3: finish AMD/biomining/REE cohort (14 communities)

[realmarcin]

Completes the AMD/biomining/REE arm of the #30 related_ingredients backfill (continues #79/#80/#81/#83).

Every related_ingredient entry uses a CHEBI term verified live against the ChEBI sqlite db via OAK, with snippets copied verbatim from cached PMID/DOI abstracts in references_cache/. No cross-repo IDs minted.

related_ingredients adoption: 19/265 → 33/265.

Communities (14)

Community	Ingredients (CHEBI-verified)
Richmond_Mine_AMD_Biofilm	pyrite, iron(2+), iron(3+), sulfate
Australian_Lead_Zinc_Polymetallic	zinc(2+), lead(2+), iron(2+)
AMD_Nitrososphaerota_Archaeal	ammonia, nitrite, urea
Bayan_Obo_REE_Tailings	cerium(3+), lanthanum(3+)
Chromium_Sulfur_Reduction	chromate(2-), elemental sulfur, sulfate
Copper_Biomining_Heap_Leach	chalcopyrite, copper(2+), iron(2+), pyrite
PGM_Spent_Catalyst_Bioleaching	thiosulfate(2-), palladium, copper(2+), ammonia
Rammelsberg_Cobalt_Nickel_Tailings	cobalt(2+), nickel(2+), iron(2+), sulfate
Panzhihua_Vanadium_Titanium_Tailings	vanadate(3-), iron(3+), copper(2+), nickel(2+)
Rifle_Uranium_Reducing	acetate, iron(3+), iron(2+), sulfate
Ion_Adsorption_REE_Indigenous	teichoic acid, phosphate
Miscanthus_REE_Tailings_Nitrogen	ammonium sulfate, ammonia, ammonium
Alaska_Tundra_Permafrost_Iron_Redox	iron(3+), iron(2+), acetate, benzoate
Drought_Rhizosphere_Iron_Actinobacteria	iron atom, phytosiderophore, carbohydrate

Also fixed an inherited wrong CHEBI id in Richmond (CHEBI:51905 is "calcein red-orange", not pyrite → CHEBI:86471, both occurrences).

⚠️ Follow-up flagged (out of scope here)

OAK verification surfaced ~24 pre-existing wrong CHEBI ids in existing metabolites blocks across these files — e.g. CHEBI:50885 labeled "chalcopyrite" is actually fludrocortisone; CHEBI:49976 "yttrium(3+)" is zinc dichloride; CHEBI:37119 "uranium(VI)" is gallanyl group. Bayan_Obo also has pre-existing fabricated MXene/Ti₃C₂Tₓ snippets mismatched to its cerium DOI. Recommend a dedicated CHEBI-cleanup PR.

Test plan

• just test → 136 passed, 9 skipped
• All 14 files validate clean (linkml-validate)

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Completes another batch of Issue #30 backfill by adding related_ingredients (CHEBI-linked with evidence snippets) to an additional set of AMD/biomining/REE-focused community KB YAMLs, and corrects a previously wrong CHEBI ID for pyrite in the Richmond Mine community.

Changes:

• Added related_ingredients blocks to 14 community YAML records (CHEBI term + relevance + EvidenceItem).
• Corrected Richmond Mine “pyrite” CHEBI ID (CHEBI:51905 → CHEBI:86471).
• Expanded coverage of metals/REE-related communities with ingredient-level linking data for cross-repo/environmental discovery.

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
kb/communities/Rifle_Uranium_Reducing_Community.yaml	Adds related_ingredients for acetate/Fe(III)/Fe(II)/sulfate with PMID evidence.
kb/communities/Richmond_Mine_AMD_Biofilm.yaml	Fixes pyrite CHEBI ID in metabolites; adds related_ingredients for pyrite/Fe(II)/Fe(III)/sulfate.
kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml	Adds related_ingredients for Co(II)/Ni(II)/Fe(II)/sulfate with DOI/PMID evidence.
kb/communities/PGM_Spent_Catalyst_Bioleaching.yaml	Adds related_ingredients for thiosulfate/Pd/Cu(II)/ammonia with PMID evidence.
kb/communities/Panzhihua_Vanadium_Titanium_Tailings.yaml	Adds related_ingredients for vanadate/Fe(III)/Cu(II)/Ni(II) with DOI/PMID evidence.
kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml	Adds related_ingredients for ammonium sulfate/ammonia/ammonium with PMID evidence.
kb/communities/Ion_Adsorption_REE_Indigenous_Community.yaml	Adds related_ingredients for teichoic acid/phosphate with PMID evidence.
kb/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml	Adds related_ingredients for iron/phytosiderophore/carbohydrate with PMID evidence.
kb/communities/Copper_Biomining_Heap_Leach.yaml	Adds related_ingredients for chalcopyrite/Cu(II)/Fe(II)/pyrite with DOI evidence.
kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml	Adds related_ingredients for chromate/elemental sulfur/sulfate with DOI evidence.
kb/communities/Bayan_Obo_REE_Tailings_Consortium.yaml	Adds related_ingredients for Ce(III)/La(III) with DOI evidence.
kb/communities/Australian_Lead_Zinc_Polymetallic.yaml	Adds related_ingredients for Zn(II)/Pb(II)/Fe(II) with PMID/DOI evidence.
kb/communities/AMD_Nitrososphaerota_Archaeal.yaml	Adds related_ingredients for ammonia/nitrite/urea with PMID evidence.
kb/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.yaml	Adds related_ingredients for Fe(III)/Fe(II)/acetate/benzoate with PMID evidence.

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