#30 backfill: gut/rhizosphere cohort batch 1 (8 communities)

[realmarcin]

Starts the gut/rhizosphere arm of the #30 related_ingredients backfill to broaden ENVO/substrate coverage (continues #90 and the metals cohort #79/#80/#81/#83).

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_ingredients adoption: 33/265 → 41/265.

Communities (8)

Community	Ingredients (CHEBI-verified)
Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism	formate, methane, acetate, fructan
SIHUMIx_Human_Intestinal_Model_Community	acetate, butyrate, carbohydrate, choline
Arabidopsis_Coumarin_Root_SynCom	coumarin, iron(3+)
Maize_Benzoxazinoid_Metabolizing_SynComs	6-methoxy-2-benzoxazolinone (MBOA)
Infant_Gut_HMO_SynCom	oligosaccharide (HMO), organic acid, carbohydrate
Engineered_Gut_Amino_Acid_CrossFeeding_Consortium	amino acid
Avena_Rhizosphere_CrossKingdom_SIP_Community	carbon dioxide (¹³C SIP substrate)
GLBRC_Exometabolite_Transwell_SynCom	antibacterial agent (exometabolite class)

Curation note

Several gut/rhizosphere abstracts name few specific compounds, so some entries fall back to broad CHEBI classes (carbohydrate, amino acid, organic acid, antibacterial agent) rather than invent specific-compound snippets. These are honest, evidence-backed, and improvable when richer references are cached. The agents OAK-verified every id and refused to fabricate specifics (DIMBOA, scopoletin, specific HMOs/SCFAs were dropped when not named verbatim in the cited abstract).

Test plan

• just test → 136 passed, 9 skipped
• All 8 files validate clean (linkml-validate)

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR continues the #30 related_ingredients backfill by adding evidence-backed ChEBI ingredient links to 8 gut/rhizosphere community records, broadening environmental and substrate coverage without changing schema or code.

Changes:

• Adds related_ingredients blocks to 8 community YAML files.
• Uses ChEBI terms plus evidence snippets for gut, rhizosphere, SynCom, and exometabolite communities.
• Omits mediaingredientmech_id, consistent with prior backfill batches where cross-repo IDs have not yet been minted.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
kb/communities/SIHUMIx_Human_Intestinal_Model_Community.yaml	Adds acetate, butyrate, carbohydrate, and choline ingredient links.
kb/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.yaml	Adds MBOA as the central benzoxazinoid substrate.
kb/communities/GLBRC_Exometabolite_Transwell_SynCom.yaml	Adds antibacterial agent/antibiotics as an exometabolite class.
kb/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.yaml	Adds amino acid as the engineered cross-feeding substrate class.
kb/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.yaml	Adds HMO-related oligosaccharide, organic acid, and carbohydrate links.
kb/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.yaml	Adds formate, methane, acetate, and fructan links for the gut mutualism.
kb/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.yaml	Adds carbon dioxide as the labeled SIP substrate.
kb/communities/Arabidopsis_Coumarin_Root_SynCom.yaml	Adds coumarin and ferric iron links for the root SynCom.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.