112 lines
3.7 KiB
Markdown
112 lines
3.7 KiB
Markdown
---
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title: "Metabolomics Workbench REST API"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/metabolomics-workbench.md
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upstream_sha: 9c9bd2e9
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imported_at: 2026-06-26
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prompt_class: prompt
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# Metabolomics Workbench REST API
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## Base URL
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```
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https://www.metabolomicsworkbench.org/rest/
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```
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## Auth
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No API key required. Fully public.
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## URL Structure
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```
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/rest/{context}/{input_item}/{input_value}/{output_item}
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```
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Contexts: `study`, `compound`, `refmet`, `gene`, `protein`, `moverz`, `exactmass`
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## Key Endpoints
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### Study Context
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| URL Pattern | Description |
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|---|---|
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| `/rest/study/study_id/{ST_ID}/summary` | Study summary metadata |
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| `/rest/study/study_id/{ST_ID}/metabolites` | Metabolites in a study |
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| `/rest/study/study_id/{ST_ID}/analysis` | Analysis details |
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| `/rest/study/study_id/{ST_ID}/factors` | Experimental factors |
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| `/rest/study/study_id/{ST_ID}/data` | Named metabolite data matrix |
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| `/rest/study/study_id/{ST_ID}/species` | Species information |
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| `/rest/study/study_id/{ST_ID}/disease` | Disease information |
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| `/rest/study/study_title/{keyword}/summary` | Search studies by title keyword |
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| `/rest/study/study_type/{type}/summary` | Search by study type |
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| `/rest/study/analysis_id/{AN_ID}/summary` | Summary by analysis ID |
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Study IDs: `ST######` (e.g., `ST000001`). Analysis IDs: `AN######`.
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### Compound Context
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| URL Pattern | Description |
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|---|---|
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| `/rest/compound/name/{NAME}/summary` | Search compound by name |
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| `/rest/compound/pubchem_cid/{CID}/summary` | Search by PubChem CID |
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| `/rest/compound/hmdb_id/{HMDB_ID}/summary` | Search by HMDB ID |
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| `/rest/compound/kegg_id/{KEGG_ID}/summary` | Search by KEGG ID |
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| `/rest/compound/inchi_key/{KEY}/summary` | Search by InChI key |
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| `/rest/compound/regno/{REGNO}/classification` | Compound classification |
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| `/rest/compound/regno/{REGNO}/molfile` | MOL file (structure) |
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### RefMet (Standardized Nomenclature)
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| URL Pattern | Description |
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|---|---|
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| `/rest/refmet/name/{NAME}/all` | Full RefMet record |
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| `/rest/refmet/match/{NAME}/name` | Match name to standardized RefMet name |
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### Gene / Protein Context
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| URL Pattern | Description |
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|---|---|
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| `/rest/gene/gene_symbol/{SYMBOL}/all` | Gene info by symbol |
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| `/rest/gene/gene_id/{ID}/all` | Gene info by Entrez ID |
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| `/rest/protein/uniprot_id/{ID}/all` | Protein by UniProt ID |
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### Mass Search (MoverZ / ExactMass)
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```
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/rest/moverz/mz/{MZ_VALUE}/tol/{TOLERANCE}/mode/{pos|neg}
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/rest/exactmass/mass/{MASS_VALUE}/tol/{TOLERANCE}
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```
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## Example Calls
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```
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# Study summary
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https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary
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# Metabolites in a study
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https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/metabolites
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# Search studies by title
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https://www.metabolomicsworkbench.org/rest/study/study_title/diabetes/summary
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# Compound by name
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https://www.metabolomicsworkbench.org/rest/compound/name/glucose/summary
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# Compound by PubChem CID
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https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5793/summary
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# RefMet standardized name match
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https://www.metabolomicsworkbench.org/rest/refmet/match/alpha-D-Glucose/name
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# m/z search in positive mode
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https://www.metabolomicsworkbench.org/rest/moverz/mz/175.0354/tol/0.005/mode/pos
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# Exact mass search
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https://www.metabolomicsworkbench.org/rest/exactmass/mass/174.0282/tol/0.005
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```
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## Response Format
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Default is JSON. `mwtab` output returns MWTab text. `molfile` returns MOL/SDF text. No pagination — full results returned.
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## Rate Limits
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No published limits. Be reasonable. Add 0.5-1s delay for batch calls.
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