Metabolomics Workbench REST API

Base URL

https://www.metabolomicsworkbench.org/rest/

Auth

No API key required. Fully public.

URL Structure

/rest/{context}/{input_item}/{input_value}/{output_item}

Contexts: study, compound, refmet, gene, protein, moverz, exactmass

Key Endpoints

Study Context

URL Pattern	Description
`/rest/study/study_id/{ST_ID}/summary`	Study summary metadata
`/rest/study/study_id/{ST_ID}/metabolites`	Metabolites in a study
`/rest/study/study_id/{ST_ID}/analysis`	Analysis details
`/rest/study/study_id/{ST_ID}/factors`	Experimental factors
`/rest/study/study_id/{ST_ID}/data`	Named metabolite data matrix
`/rest/study/study_id/{ST_ID}/species`	Species information
`/rest/study/study_id/{ST_ID}/disease`	Disease information
`/rest/study/study_title/{keyword}/summary`	Search studies by title keyword
`/rest/study/study_type/{type}/summary`	Search by study type
`/rest/study/analysis_id/{AN_ID}/summary`	Summary by analysis ID

Study IDs: ST###### (e.g., ST000001). Analysis IDs: AN######.

Compound Context

URL Pattern	Description
`/rest/compound/name/{NAME}/summary`	Search compound by name
`/rest/compound/pubchem_cid/{CID}/summary`	Search by PubChem CID
`/rest/compound/hmdb_id/{HMDB_ID}/summary`	Search by HMDB ID
`/rest/compound/kegg_id/{KEGG_ID}/summary`	Search by KEGG ID
`/rest/compound/inchi_key/{KEY}/summary`	Search by InChI key
`/rest/compound/regno/{REGNO}/classification`	Compound classification
`/rest/compound/regno/{REGNO}/molfile`	MOL file (structure)

RefMet (Standardized Nomenclature)

URL Pattern	Description
`/rest/refmet/name/{NAME}/all`	Full RefMet record
`/rest/refmet/match/{NAME}/name`	Match name to standardized RefMet name

Gene / Protein Context

URL Pattern	Description
`/rest/gene/gene_symbol/{SYMBOL}/all`	Gene info by symbol
`/rest/gene/gene_id/{ID}/all`	Gene info by Entrez ID
`/rest/protein/uniprot_id/{ID}/all`	Protein by UniProt ID

Mass Search (MoverZ / ExactMass)

/rest/moverz/mz/{MZ_VALUE}/tol/{TOLERANCE}/mode/{pos|neg}
/rest/exactmass/mass/{MASS_VALUE}/tol/{TOLERANCE}

Example Calls

# Study summary
https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary

# Metabolites in a study
https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/metabolites

# Search studies by title
https://www.metabolomicsworkbench.org/rest/study/study_title/diabetes/summary

# Compound by name
https://www.metabolomicsworkbench.org/rest/compound/name/glucose/summary

# Compound by PubChem CID
https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5793/summary

# RefMet standardized name match
https://www.metabolomicsworkbench.org/rest/refmet/match/alpha-D-Glucose/name

# m/z search in positive mode
https://www.metabolomicsworkbench.org/rest/moverz/mz/175.0354/tol/0.005/mode/pos

# Exact mass search
https://www.metabolomicsworkbench.org/rest/exactmass/mass/174.0282/tol/0.005

Response Format

Default is JSON. mwtab output returns MWTab text. molfile returns MOL/SDF text. No pagination — full results returned.

Rate Limits

No published limits. Be reasonable. Add 0.5-1s delay for batch calls.