#30 backfill: syntrophy/methanogenesis cohort batch 1 (10 communities)

[realmarcin]

Starts the syntrophy/methanogenesis arm of the #30 related_ingredients backfill. This cohort backfilled richly — all entries are specific named compounds (no broad-class fallbacks).

Every CHEBI id verified live against the ChEBI sqlite db via OAK; snippets copied verbatim from cached PMID/DOI abstracts.

related_ingredients adoption: 46/265 → 56/265.

Communities (10)

Community	Ingredients (CHEBI-verified)
Syntrophobacter_Methanobacterium_Syntrophy	propionate, formate, dihydrogen
Syntrophobacter_Methanospirillum_Syntrophy	propionate, dihydrogen, formate
Syntrophomonas_Methanospirillum_Syntrophy	butyrate, acetate, dihydrogen
Syntrophomonas_Methanococcus_Butyrate_Coculture	butyrate, dihydrogen, methane
Pelotomaculum_Methanothermobacter_Syntrophy	propionate
Pelotomaculum_Methanocella_Propionate_RNASeq	propionate, formate, dihydrogen, methane
Desulfovibrio_Methanococcus_Syntrophy	lactate, dihydrogen
Desulfovibrio_Methanosarcina_Lactate_Syntrophy	lactate, acetate, dihydrogen, methane
Geobacter_Methanosaeta_DIET	ethanol, carbon dioxide, methane
Geobacter_Methanosarcina_DIET	ethanol, acetate, methane, carbon dioxide

Compounds were dropped (not invented) where the cited+cached abstract had no verbatim mention.

⚠️ Pre-existing CHEBI bugs flagged (out of scope, growth_media this time)

Syntrophomonas_Methanospirillum (CHEBI:88613 sodium butyrate → a PI lipid; CHEBI:87157 sodium sulfide → a morpholine; CHEBI:32447 L-cysteine HCl → L-cysteinyl group; CHEBI:48953 resazurin → cyclohexenones) and both Geobacter DIET files (CHEBI:35235 L-cysteine → zwitterion; CHEBI:85357 sodium sulfide → unrelated). Added to the running cleanup list.

Test plan

• just test → 136 passed, 9 skipped
• All 10 files validate clean (linkml-validate)

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Backfills the new related_ingredients field on ten syntrophy/methanogenesis community YAML records, completing the first batch of the #30 backfill effort. Each entry references a CHEBI-verified ingredient and cites a verbatim snippet from a cached PMID/DOI abstract.

Changes:

• Add related_ingredients blocks (1–4 entries each) to ten community files, naming compounds such as propionate, butyrate, lactate, ethanol, formate, dihydrogen, acetate, carbon dioxide, and methane.
• Each ingredient entry includes chebi_term (id/label), relevance, and at least one evidence item with reference, supports, evidence_source, snippet, and explanation.
• Raises related_ingredients adoption from 46/265 to 56/265 communities.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
kb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml	Adds propionate, formate, dihydrogen entries
kb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml	Adds propionate, dihydrogen, formate entries
kb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml	Adds butyrate, acetate, dihydrogen entries
kb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml	Adds butyrate, dihydrogen, methane entries
kb/communities/Pelotomaculum_Methanothermobacter_Syntrophy.yaml	Adds propionate entry
kb/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.yaml	Adds propionate, formate, dihydrogen, methane entries
kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml	Adds lactate, dihydrogen entries
kb/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.yaml	Adds lactate, acetate, dihydrogen, methane entries
kb/communities/Geobacter_Methanosaeta_DIET.yaml	Adds ethanol, carbon dioxide, methane entries
kb/communities/Geobacter_Methanosarcina_DIET.yaml	Adds ethanol, acetate, methane, carbon dioxide entries

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