Metabolomics Workbench Database — REST API Access

Overview

The Metabolomics Workbench (MW) REST API at https://www.metabolomicsworkbench.org/rest/ exposes 4,200+ metabolomics studies hosted at UCSD under NIH Common Fund sponsorship. URL pattern is /{context}/{input_item}/{input_value}/{output_item}/{format}. Contexts include compound, refmet, moverz, study, analysis, metabolite, gene, protein. Notable quirks discovered live:

• compound/name/{x} is rejected — name is not an allowed input_item. Use pubchem_cid, kegg_id, inchi_key, hmdb_id, regno, lm_id, formula, smiles, or abbrev. For free-text input, go through refmet/match/{x} first.
• refmet/name/{x}/all requires the exact RefMet name (e.g. Glucose, not D-glucose); use refmet/match/{x} for fuzzy normalisation first.
• moverz/{REFMET|LIPIDS|MB}/{mz}/{ion}/{tol}/txt returns TSV text (no JSON variant).
• The metstat/filter/... endpoint shown in older examples returns [] — replace with study/{context}/{value}/summary (or /metabolites) + client-side filtering.

No authentication required.

When to Use