Metabolomics Workbench Database — REST API Access

Overview

Query the Metabolomics Workbench (MW) REST API to access 4,200+ metabolomics studies hosted at UCSD under NIH Common Fund sponsorship. The API provides six query contexts: compound/metabolite lookups, study metadata and experimental data retrieval, RefMet standardized nomenclature, MetStat study filtering by species/disease/analysis type, m/z precursor ion searches for compound identification, and gene/protein annotation from the Metabolomics Gene/Protein (MGP) database.

When to Use

• Searching for metabolite structures, identifiers, or chemical properties by PubChem CID, KEGG ID, InChI key, or formula
• Discovering metabolomics studies by species, disease, analysis type, or polarity
• Standardizing metabolite names to RefMet nomenclature for cross-study comparison
• Identifying unknown compounds from mass spectrometry m/z values with adduct type matching
• Retrieving experimental metabolomics data (concentrations, abundances) from published studies
• Querying gene or protein annotations linked to metabolomics pathways
• Downloading study data in mwTab format for local analysis
• For local metabolite database parsing (220K+ entries, NMR/MS spectra) use hmdb-database instead
• For live compound property searches (110M+ compounds) use pubchem-compound-search instead

Prerequisites