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tooluniverse-metabolomics-pathway

Maps metabolites to pathways, enzymes, genes, and disease associations across HMDB, KEGG, Reactome, and MetaCyc.

1.7k|254|Updated Mar 3, 2025
Search Tags:#metabolomics#pathway analysis#metabolite identification#Reactome#kegg#disease association#bridgedb
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-metabolomics-pathway
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-metabolomics-pathway
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-metabolomics-pathway
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-metabolomics-pathway

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Connecting a metabolite of interest to its biological pathways, processing enzymes, and disease associations requires querying many disconnected databases (HMDB, KEGG, ChEBI, Reactome, MetaCyc, CTD) with incompatible identifier systems. This Skill provides a structured workflow that resolves metabolite identities, converts identifiers via BridgeDb, and chains database lookups into a coherent metabolite-to-pathway-to-disease analysis.

Core Features & Use Cases

  • Metabolite Identification & Resolution: Search by name, formula, m/z, or exact mass via PubChem-backed tools and MetabolomicsWorkbench, then cross-reference IDs with BridgeDb.
  • Pathway Mapping & Enrichment: Map compounds to MetaCyc, KEGG, and Reactome pathways and run Reactome pathway enrichment on linked gene sets.
  • Enzyme/Gene & Disease Linkage: Connect metabolites to interacting genes via CTD and retrieve curated disease associations with an evidence-grading scheme.
  • Use Case: Given an unidentified LC-MS peak at m/z 181.07, resolve it to caffeine, map it to KEGG and Reactome pathways, identify its metabolizing enzymes (e.g., CYP1A2), and compile curated disease associations from CTD.

Quick Start

Use the metabolomics pathway skill to identify the metabolite pyruvate, map it to KEGG and Reactome pathways, and list its associated enzymes and diseases.

Frequently Asked Questions about tooluniverse-metabolomics-pathway

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I map a metabolite to KEGG and Reactome pathways?▼

First resolve the metabolite identity with Metabolite_search or Metabolite_get_info, then convert its ID with BridgeDb_xrefs to obtain KEGG or ChEBI identifiers. Use KEGG_get_compound or ReactomeContent_search to retrieve the pathways it participates in.

How to identify an unknown metabolite from m/z mass spec data?▼

Use MetabolomicsWorkbench_search_by_mz with the m/z value, adduct type (e.g., M+H), and a mass tolerance to query the RefMet database. If that fails, try search_by_exact_mass or fall back to name-based searches with Metabolite_search.

Can I use HMDB IDs directly with CTD disease queries?▼

No, CTD_get_chemical_diseases accepts common chemical names, MeSH terms, or CAS numbers, not HMDB IDs. Convert the HMDB entry to a common name first, or use Metabolite_get_diseases which accepts HMDB IDs and PubChem CIDs directly.

Why does Reactome pathway enrichment fail with my metabolite list?▼

ReactomeAnalysis_pathway_enrichment expects gene or protein identifiers passed as a space-separated string, not an array and not metabolite IDs. Convert metabolites to interacting genes via CTD_get_chemical_gene_interactions before running enrichment.

What are the limitations of HMDB-based metabolite lookups?▼

HMDB has no open API, so lookups go through Metabolite_get_info, which is PubChem-backed and returns HMDB IDs, InChIKeys, and classifications. Coverage depends on the metabolite being cross-referenced in PubChem or BridgeDb mapping databases.

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