tooluniverse-metabolomics-pathway
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, orReactomeContent_search - Cross-database IDs: use
BridgeDb_xrefs - Enzyme-metabolite relationships: use
CTD_get_chemical_gene_interactionsorKEGG_get_compound - Disease associations: query
Metabolite_get_diseasesorCTD_get_chemical_diseases
COMPUTE, DON'T DESCRIBE
When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.
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