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tooluniverse-metabolomics-pathway
Metabolomics pathway analysis — metabolite identification (HMDB, KEGG, ChEBI), pathway mapping (Reactome, KEGG, MetaCyc), disease associations, enzyme/gene linkage. Use for metabolite-to-pathway-to-disease connections, BridgeDb-based ID conversion, and integrating metabolomics with gene-level pathway analyses.
plugin/skills/tooluniverse-metabolomics-pathway/SKILL.md
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# Metabolomics Pathway Analysis
Identify metabolites, map to metabolic pathways, find disease associations, and connect to enzymes/genes.
## Domain Reasoning
Metabolite-to-pathway mapping requires correct, database-specific identifiers. HMDB IDs link to KEGG/Reactome but must be converted via BridgeDb; PubChem CIDs need explicit cross-referencing. Always verify metabolite identity first: the same common name can refer to structurally distinct isomers, and PubChem names frequently differ from CTD/KEGG names.
## LOOK UP DON'T GUESS
- Pathway membership: call `MetaCyc_get_compound`, `KEGG_get_compound`, or `ReactomeContent_search`
- Cross-database IDs: use `BridgeDb_xrefs`
- Enzyme-metabolite relationships: use `CTD_get_chemical_gene_interactions` or `KEGG_get_compound`
- Disease associations: query `Metabolite_get_diseases` or `CTD_get_chemical_diseases`