metabolomics-workbench-database
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-databaseinstead - For live compound property searches (110M+ compounds) use
pubchem-compound-searchinstead
Prerequisites
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