drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/metabolomics-workbench.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Metabolomics Workbench REST API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/metabolomics-workbench.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

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.