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tooluniverse-metabolomics

Annotate metabolites and search metabolomics studies across HMDB, MetaboLights, and PubChem databases.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires tooluniverse, and includes scripts (resource) components.

What problem does it solve?

Identifying metabolites from mass-spec experiments and finding relevant metabolomics studies requires manually querying multiple databases (HMDB, MetaboLights, Metabolomics Workbench, PubChem) and stitching results together. This Skill automates that multi-database lookup and compiles findings into a structured markdown research report.

Core Features & Use Cases

  • Metabolite Identification & Annotation: Search HMDB by metabolite name to retrieve HMDB IDs, chemical formulas, molecular weights, and pathways, with automatic PubChem fallback for CID and SMILES data.
  • Study Retrieval & Search: Fetch study details from MetaboLights (MTBLS IDs) or Metabolomics Workbench (ST IDs), and search studies by disease, compound, or method keywords.
  • Structured Report Generation: Run a 4-phase pipeline (identification, study details, study search, database overview) that writes a markdown report with confidence-level guidance (L1-L4) for metabolite identification.
  • Use Case: Given a list of detected metabolites like glucose, lactate, and pyruvate from an LC-MS experiment, generate an annotated report with HMDB IDs, formulas, pathways, and related diabetes studies from MetaboLights.

Quick Start

Ask the AI to analyze the metabolites glucose, lactate, and pyruvate, retrieve study MTBLS1, and generate a metabolomics research report.

Frequently Asked Questions about tooluniverse-metabolomics

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

FAQPage Schema
How do I annotate metabolites with HMDB IDs and pathways?▼

Provide a list of metabolite names to the analysis pipeline, which searches HMDB for each compound and retrieves HMDB IDs, chemical formulas, molecular weights, and pathway annotations. If HMDB has no match, it falls back to PubChem for CID and SMILES data.

How to search MetaboLights for metabolomics studies by disease?▼

Pass a search query such as a disease name or method keyword to the metabolights_search_studies tool. The pipeline returns matching study IDs with previews and the total result count, which are compiled into the report's study search section.

Why does HMDB search return 'Error querying HMDB: 0'?▼

This error means the HMDB search returned empty results, typically for uncommon metabolite names or synonyms. HMDB tools are SOAP-based and require an operation parameter; the pipeline automatically falls back to PubChem when HMDB yields no match.

Does this metabolomics workflow require API keys?▼

Most metabolomics tools including HMDB, MetaboLights, Metabolomics Workbench, and PubChem work without API keys. The .env.template file lists optional keys for other ToolUniverse databases, but missing keys only produce an informational warning.

What are the limitations for large metabolite lists?▼

Reports automatically limit output to the first 10 metabolites to keep files readable, and each metabolite is queried individually so large lists run slowly. For more than 20 metabolites, batch the input into groups of 10 and generate separate reports.

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