#30 backfill: gut/rhizosphere cohort batch 2 (5 communities)#92
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realmarcin wants to merge 1 commit into
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#30 backfill: gut/rhizosphere cohort batch 2 (5 communities)#92realmarcin wants to merge 1 commit into
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Continues the gut/rhizosphere arm of the #30 related_ingredients backfill. Every entry uses a CHEBI term verified live against the ChEBI sqlite db via OAK, with snippets copied verbatim from cached PMID/DOI abstracts. No cross-repo IDs. related_ingredients adoption: 41/265 -> 46/265. | Community | Ingredients (CHEBI-verified) | |---|---| | Tomato_Oxylipin_SynCom3 | oxylipin, colneleic acid, colnelenic acid | | Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota | glucose, triglyceride | | Honeybee_Core20_Defined_Microbiota | carbohydrate, phosphoenolpyruvate | | Soybean_N_Fixation_sfSynCom | N-acyl-L-homoserine lactone | | Medicago_Nodule_Biofertilizer_SynCom | dinitrogen | Batch B also screened OMM12, hCom2, and Altered_Schaedler_Flora, but their only cached references are stubs (title + prior snippets, no abstract body), so no verbatim-supportable ingredient exists; left unchanged rather than inventing snippets. They need full abstracts re-fetched into references_cache first. Pre-existing CHEBI bug flagged (out of scope): Soybean_N_Fixation metabolites use CHEBI:48850 for "N-acyl-L-homoserine lactone", but that id is alkyloxynaphthalene; correct id is CHEBI:55474 (used in the new block). Test plan: just test (136 passed, 9 skipped), all 5 files validate clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Pull request overview
Continues the CommunityMech KB curation for Issue #30 by backfilling related_ingredients for a gut/rhizosphere cohort batch (5 communities), linking each community to CHEBI-grounded ingredient terms with publication-quote evidence.
Changes:
- Added
related_ingredientsblocks (CHEBI term + relevance + evidence) to 5 existing community YAML records. - Expanded ingredient coverage for gut/rhizosphere communities with additional evidence snippets anchored to PMIDs.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| kb/communities/Tomato_Oxylipin_SynCom3.yaml | Adds oxylipin/divinyl-ether related ingredients with PMID-backed evidence. |
| kb/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.yaml | Adds glucose and triglyceride as host metabolite readouts tied to colonization. |
| kb/communities/Honeybee_Core20_Defined_Microbiota.yaml | Adds carbohydrate and phosphoenolpyruvate as functionally relevant gut substrates/metabolites. |
| kb/communities/Soybean_N_Fixation_sfSynCom.yaml | Adds AHL-related ingredient entry (CHEBI-linked) with quorum-sensing evidence. |
| kb/communities/Medicago_Nodule_Biofertilizer_SynCom.yaml | Adds dinitrogen as a related ingredient with nodulation/nitrogen-content evidence. |
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| - reference: PMID:37299063 | ||
| supports: SUPPORT | ||
| evidence_source: IN_VIVO | ||
| snippet: nodulation (from 1.5- to 3-fold increase in nodules number), photosynthesis and | ||
| nitrogen content (up to 4-fold under metal stress) under all the controlled conditions | ||
| tested | ||
| explanation: The increase in nodulation and plant nitrogen content reflects symbiotic | ||
| dinitrogen fixation by the nodule-forming rhizobial members of the SynCom. |
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| related_ingredients: | ||
| - preferred_term: N-acyl-L-homoserine lactone | ||
| chebi_term: | ||
| id: CHEBI:55474 | ||
| label: N-acyl-L-homoserine lactone |
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Continues the gut/rhizosphere arm of the #30
related_ingredientsbackfill (follows #91).Every entry uses a CHEBI term verified live against the ChEBI sqlite db via OAK, with snippets copied verbatim from cached PMID/DOI abstracts.
related_ingredientsadoption: 41/265 → 46/265.Communities (5)
Curation note
Batch B also screened OMM12, hCom2, and Altered_Schaedler_Flora, but their only cached references are stubs (title + previously-used snippets, no abstract body), so no verbatim-supportable ingredient exists — left unchanged rather than inventing. They need full abstracts re-fetched into
references_cache/first.Soybean_N_Fixation_sfSynCommetabolitesuseCHEBI:48850for "N-acyl-L-homoserine lactone", but that id is alkyloxynaphthalene; correct id isCHEBI:55474(used in the new block). Adds to the running CHEBI-cleanup list.Test plan
just test→ 136 passed, 9 skippedlinkml-validate)🤖 Generated with Claude Code