#30 backfill: electroactive/MFC peripheral set (4 communities)#96
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realmarcin wants to merge 1 commit into
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#30 backfill: electroactive/MFC peripheral set (4 communities)#96realmarcin wants to merge 1 commit into
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Closes the electroactive/MFC tail of the syntrophy/methanogenesis work. CHEBI ids verified live via OAK; snippets verbatim from cached abstracts. related_ingredients adoption: 65/265 -> 69/265. | Community | Ingredients (CHEBI-verified) | |---|---| | Rhodopseudomonas_Geobacter_Magnetite_Redox | magnetite, iron(2+), iron(3+) | | Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC | cellulose [(1->4)-beta-D-glucan], acetate, ethanol, dihydrogen | | Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding | methane, acetate, methanol | | High_Solids_Switchgrass_Methanogenic_Microbiome | lignocellulose, dihydrogen, methane | Shewanella_Geobacter_Exoelectrogenic_Biofilm left unchanged: its one cached reference names only generic "organic substrates", nothing verbatim-supportable. Pre-existing CHEBI label issues flagged (out of scope): CHEBI:18246 is labeled "cellulose" in several files but its canonical label is "(1->4)-beta-D-glucan"; CHEBI:37686 "xylan" is alpha-D-allose; CHEBI:50821 "iron(II,III) oxide" canonical label is "ferrosoferric oxide". Added to the cleanup list. Test plan: just test (136 passed, 9 skipped), all 4 files validate clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR continues the related_ingredients backfill for the electroactive/MFC peripheral set by adding CHEBI-linked ingredient descriptors (with evidence snippets) to four existing community YAML records.
Changes:
- Added
related_ingredientsblocks for magnetite/Fe redox cycling, methane/acetate/methanol cross-feeding, lignocellulose → H₂/CH₄ methanogenesis, and cellulose MFC coculture metabolites. - Included per-ingredient relevance narratives and supporting evidence items (PMID/DOI + verbatim snippet + explanation).
- Preserved existing community content while extending metadata for discovery/cross-repo linkage.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| kb/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.yaml | Adds related_ingredients for magnetite and Fe(II)/Fe(III) redox cycling with literature evidence. |
| kb/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.yaml | Adds related_ingredients for methane/acetate/methanol tied to the cross-feeding narrative and evidence. |
| kb/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.yaml | Adds related_ingredients for lignocellulose, H₂, and methane with metaproteomics/reactor product evidence. |
| kb/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.yaml | Adds related_ingredients for cellulose fermentation products supporting anode respiration with evidence. |
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| - preferred_term: magnetite | ||
| chebi_term: | ||
| id: CHEBI:46726 | ||
| label: magnetite |
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| chebi_term: | ||
| id: CHEBI:18246 | ||
| label: (1->4)-beta-D-glucan |
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Closes the electroactive/MFC tail of the syntrophy/methanogenesis work (follows #94/#95). CHEBI ids verified live via OAK; snippets verbatim from cached abstracts.
related_ingredientsadoption: 65/265 → 69/265.Shewanella_Geobacter_Exoelectrogenic_Biofilmleft unchanged — its one cached reference names only generic "organic substrates", nothing verbatim-supportable.CHEBI:18246is labeled "cellulose" in several files but its canonical label is "(1->4)-beta-D-glucan";CHEBI:37686"xylan" is alpha-D-allose;CHEBI:50821"iron(II,III) oxide" canonical label is "ferrosoferric oxide". Added to the running cleanup list.Test plan
just test→ 136 passed, 9 skippedlinkml-validate)🤖 Generated with Claude Code