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

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.