Tooluniverse Metabolomics

This is a multi-database metabolomics research tool that pulls from HMDB, MetaboLights, Metabolomics Workbench, and PubChem to annotate metabolites and find studies. Feed it a list of metabolites like glucose or lactate and it returns HMDB IDs, chemical properties, and pathway information in a structured markdown report. You can also search for studies by disease or keyword, or pull specific study details using IDs like MTBLS1. It's built around a four-phase pipeline that handles identification, study retrieval, search, and database overviews. Useful if you're doing mass spec annotation or need to quickly map metabolites to pathways without clicking through multiple web interfaces. The SOAP-based HMDB tools require special handling, which the skill manages automatically.

skills.sh installs: 358
GitHub stars: 1.8K
last updated: Aug 21, 2026

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Install

$ npx -y skills add mims-harvard/tooluniverse --skill tooluniverse-metabolomics --agent claude-code

Installs into .claude/skills of the current project.

Files

Metabolomics Research

Comprehensive metabolomics research skill that identifies metabolites, analyzes studies, and searches metabolomics databases. Generates structured research reports with annotated metabolite information, study details, and database statistics.

Use Case

Use this skill when asked to:

Identify or annotate metabolites (HMDB IDs, chemical properties, pathways)
Retrieve metabolomics study information from MetaboLights or Metabolomics Workbench
Search for metabolomics studies by keywords or disease
Analyze metabolite profiles or datasets
Generate comprehensive metabolomics research reports

Example queries: