Metabolomics Workbench Database

This gives you programmatic access to NIH's Metabolomics Workbench, which hosts over 4,200 metabolomics studies with MS and NMR data. You can search by m/z values with different ion adducts, standardize metabolite names through RefMet, pull study datasets, and filter by experimental parameters like LCMS vs GCMS or sample type. Particularly useful if you're doing biomarker discovery or need to cross-reference metabolites across KEGG, HMDB, and PubChem identifiers. The REST API is straightforward and returns JSON, so you can quickly build queries to find which studies measured specific compounds or identify unknowns from mass spec data. Good coverage of the main use cases for computational metabolomics work.

skills.sh installs: 264
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill metabolomics-workbench-database --agent claude-code

Installs into .claude/skills of the current project.

Files

Metabolomics Workbench Database

Overview

The Metabolomics Workbench is a comprehensive NIH Common Fund-sponsored platform hosted at UCSD that serves as the primary repository for metabolomics research data. It provides programmatic access to over 4,200 processed studies (3,790+ publicly available), standardized metabolite nomenclature through RefMet, and powerful search capabilities across multiple analytical platforms (GC-MS, LC-MS, NMR).

When to Use This Skill

This skill should be used when querying metabolite structures, accessing study data, standardizing nomenclature, performing mass spectrometry searches, or retrieving gene/protein-metabolite associations through the Metabolomics Workbench REST API.