Backfill related_ingredients via NCBI BioC full-text re-fetch (hCom2, Cheese_Rind) (#30)

kb/communities/Cheese_Rind_InSitu_InVitro_Model_Community.yaml

@@ -206,4 +206,79 @@ associated_datasets:
     evidence_source: IN_VIVO
     snippet: Sequencing of 137 different rind communities across 10 countries
     explanation: Supports the dataset scope and sampling scale.
+related_ingredients:
+- preferred_term: valine
+  chebi_term:
+    id: CHEBI:27266
+    label: valine
+  relevance: >
+    Branched-chain amino acid degraded by the rind community, contributing to
+    volatile (sweaty) aroma compounds.
+  evidence:
+  - reference: PMID:25036636
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: Pathways for valine, leucine, and isoleucine degradation
+    explanation: Names valine among the branched-chain amino acids degraded by the community.
+- preferred_term: leucine
+  chebi_term:
+    id: CHEBI:25017
+    label: leucine
+  relevance: >
+    Branched-chain amino acid degraded by the rind community, contributing to aroma.
+  evidence:
+  - reference: PMID:25036636
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: Pathways for valine, leucine, and isoleucine degradation
+    explanation: Names leucine among the branched-chain amino acids degraded by the community.
+- preferred_term: isoleucine
+  chebi_term:
+    id: CHEBI:24898
+    label: isoleucine
+  relevance: >
+    Branched-chain amino acid degraded by the rind community, contributing to aroma.
+  evidence:
+  - reference: PMID:25036636
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: Pathways for valine, leucine, and isoleucine degradation
+    explanation: Names isoleucine among the branched-chain amino acids degraded by the community.
+- preferred_term: cysteine
+  chebi_term:
+    id: CHEBI:15356
+    label: cysteine
+  relevance: >
+    Sulfur-containing amino acid whose metabolism by the community yields pungent
+    volatile sulfur compounds characteristic of cheese rinds.
+  evidence:
+  - reference: PMID:25036636
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: Cysteine and methionine metabolism
+    explanation: Names cysteine among the sulfur amino acids metabolized for aroma.
+- preferred_term: methionine
+  chebi_term:
+    id: CHEBI:16811
+    label: methionine
+  relevance: >
+    Sulfur-containing amino acid metabolized by the community to volatile sulfur compounds.
+  evidence:
+  - reference: PMID:25036636
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: Cysteine and methionine metabolism
+    explanation: Names methionine among the sulfur amino acids metabolized for aroma.
+- preferred_term: methanethiol
+  chebi_term:
+    id: CHEBI:16007
+    label: methanethiol
+  relevance: >
+    Volatile sulfur compound enriched in these rind communities, a key cheese aroma product.
+  evidence:
+  - reference: PMID:25036636
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: methanethiol, are enriched in these communities
+    explanation: Anchors methanethiol as a volatile sulfur product of the rind community.
 metal_relevance: NOT_APPLICABLE

kb/communities/hCom2_Complex_Gut_Microbiome.yaml

@@ -57,3 +57,127 @@ environmental_factors:
     colonization resistance.
   evidence:
   - *id001
+related_ingredients:
+- preferred_term: arginine
+  chebi_term:
+    id: CHEBI:29016
+    label: arginine
+  relevance: >
+    Arginine is fermented by hCom2 members via the arginine deiminase pathway,
+    a defined amino-acid-utilization route in the community.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: conversion of arginine to ornithine plus CO2 and two equivalents of ammonium
+    explanation: Anchors arginine as the substrate of the community's arginine deiminase pathway.
+- preferred_term: ornithine
+  chebi_term:
+    id: CHEBI:18257
+    label: ornithine
+  relevance: >
+    Ornithine is the product of arginine catabolism via the arginine deiminase pathway in hCom2.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: conversion of arginine to ornithine plus CO2 and two equivalents of ammonium
+    explanation: Anchors ornithine as the product of arginine deiminase activity.
+- preferred_term: carbon dioxide
+  chebi_term:
+    id: CHEBI:16526
+    label: carbon dioxide
+  relevance: >
+    CO2 is released during arginine fermentation by the community.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: conversion of arginine to ornithine plus CO2 and two equivalents of ammonium
+    explanation: Anchors CO2 as a product of the arginine deiminase pathway.
+- preferred_term: ammonium
+  chebi_term:
+    id: CHEBI:28938
+    label: ammonium
+  relevance: >
+    Ammonium is generated during arginine fermentation by the community.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: conversion of arginine to ornithine plus CO2 and two equivalents of ammonium
+    explanation: Anchors ammonium as a product of the arginine deiminase pathway.
+- preferred_term: methionine
+  chebi_term:
+    id: CHEBI:16811
+    label: methionine
+  relevance: >
+    Methionine is among the amino acids whose removal affected growth of hCom2 strains,
+    indicating community amino-acid utilization.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: methionine, histidine, isoleucine, arginine, valine, and tyrosine removal
+    explanation: Names methionine among the amino acids hCom2 strains depend on.
+- preferred_term: histidine
+  chebi_term:
+    id: CHEBI:27570
+    label: histidine
+  relevance: >
+    Histidine is among the amino acids whose removal affected growth of hCom2 strains.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: methionine, histidine, isoleucine, arginine, valine, and tyrosine removal
+    explanation: Names histidine among the amino acids hCom2 strains depend on.
+- preferred_term: isoleucine
+  chebi_term:
+    id: CHEBI:24898
+    label: isoleucine
+  relevance: >
+    Isoleucine is among the amino acids whose removal affected growth of hCom2 strains.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: methionine, histidine, isoleucine, arginine, valine, and tyrosine removal
+    explanation: Names isoleucine among the amino acids hCom2 strains depend on.
+- preferred_term: valine
+  chebi_term:
+    id: CHEBI:27266
+    label: valine
+  relevance: >
+    Valine is among the amino acids whose removal affected growth of hCom2 strains.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: methionine, histidine, isoleucine, arginine, valine, and tyrosine removal
+    explanation: Names valine among the amino acids hCom2 strains depend on.
+- preferred_term: tyrosine
+  chebi_term:
+    id: CHEBI:18186
+    label: tyrosine
+  relevance: >
+    Tyrosine is among the amino acids whose removal affected growth of hCom2 strains.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: methionine, histidine, isoleucine, arginine, valine, and tyrosine removal
+    explanation: Names tyrosine among the amino acids hCom2 strains depend on.
+- preferred_term: bile acid
+  chebi_term:
+    id: CHEBI:3098
+    label: bile acid
+  relevance: >
+    Primary and secondary bile acids in the gut are transformed by the community;
+    fecal bile-acid levels were used to compare hCom2 to a native microbiome.
+  evidence:
+  - reference: PMID:36070752
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: primary and secondary bile acid levels in feces
+    explanation: Anchors bile acids as community-transformed gut metabolites.