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metabolomics-workbench.md

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1# Metabolomics Workbench REST API

Metabolomics Workbench REST API

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3## Base URL

4```

5https://www.metabolomicsworkbench.org/rest/

6```

Base URL

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

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8## Auth

9No API key required. Fully public.

Auth

No API key required. Fully public.

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11## URL Structure

12```

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

14```

16Contexts: `study`, `compound`, `refmet`, `gene`, `protein`, `moverz` (`exactmass` is an input item, not a context)

URL Structure

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

Contexts: study, compound, refmet, gene, protein, moverz (exactmass is an input item, not a context)

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18## Key Endpoints

Key Endpoints

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20### Study Context

21| URL Pattern | Description |

22|---|---|

23| `/rest/study/study_id/{ST_ID}/summary` | Study summary metadata |

24| `/rest/study/study_id/{ST_ID}/metabolites` | Metabolites in a study |

25| `/rest/study/study_id/{ST_ID}/analysis` | Analysis details |

26| `/rest/study/study_id/{ST_ID}/factors` | Experimental factors |

27| `/rest/study/study_id/{ST_ID}/data` | Named metabolite data matrix |

28| `/rest/study/study_title/{keyword}/summary` | Search studies by title keyword |

29| `/rest/study/analysis_id/{AN_ID}/summary` | Summary by analysis ID |

31Study IDs: `ST######` (e.g., `ST000001`). Analysis IDs: `AN######`.

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_title/{keyword}/summary`	Search studies by title keyword
`/rest/study/analysis_id/{AN_ID}/summary`	Summary by analysis ID

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

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33### Compound Context

34| URL Pattern | Description |

35|---|---|

36| `/rest/compound/formula/{FORMULA}/all` | Search compound by molecular formula |

37| `/rest/compound/pubchem_cid/{CID}/all` | Search by PubChem CID |

38| `/rest/compound/hmdb_id/{HMDB_ID}/all` | Search by HMDB ID |

39| `/rest/compound/kegg_id/{KEGG_ID}/all` | Search by KEGG ID |

40| `/rest/compound/inchi_key/{KEY}/all` | Search by InChI key |

41| `/rest/compound/regno/{REGNO}/classification` | Compound classification |

42| `/rest/compound/regno/{REGNO}/molfile` | MOL file (structure) |

Compound Context

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

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44### RefMet (Standardized Nomenclature)

45| URL Pattern | Description |

46|---|---|

47| `/rest/refmet/name/{NAME}/all` | Full RefMet record |

48| `/rest/refmet/match/{NAME}/name` | Match name to standardized RefMet name |

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

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50### Gene / Protein Context

51| URL Pattern | Description |

52|---|---|

53| `/rest/gene/gene_symbol/{SYMBOL}/all` | Gene info by symbol |

54| `/rest/gene/gene_id/{ID}/all` | Gene info by Entrez ID |

55| `/rest/protein/uniprot_id/{ID}/all` | Protein by UniProt ID |

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

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57### Mass search

59The moverz input encodes library, m/z, adduct and tolerance in Daltons:

60```text

61/rest/moverz/MB/635.52/M+H/0.5

62```

63`MB` selects the Metabolomics Workbench library. Encode a plus sign as `%2B`

64when a client treats it as a space. Specify the ion/adduct; a positive/negative

65mode label alone is not sufficient. Exact mass for a lipid abbreviation is:

66```text

67/rest/moverz/exactmass/PC(34:1)/M+H

68```

Mass search

The moverz input encodes library, m/z, adduct and tolerance in Daltons:

/rest/moverz/MB/635.52/M+H/0.5

MB selects the Metabolomics Workbench library. Encode a plus sign as %2B when a client treats it as a space. Specify the ion/adduct; a positive/negative mode label alone is not sufficient. Exact mass for a lipid abbreviation is:

/rest/moverz/exactmass/PC(34:1)/M+H

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70## Example Calls

72```

73# Study summary

74https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary

76# Metabolites in a study

77https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/metabolites

79# Search studies by title

80https://www.metabolomicsworkbench.org/rest/study/study_title/diabetes/summary

82# Compounds with a formula (not unique chemical identity)

83https://www.metabolomicsworkbench.org/rest/compound/formula/C6H12O6/all

85# Compound by PubChem CID

86https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5793/all

88# RefMet standardized name match

89https://www.metabolomicsworkbench.org/rest/refmet/match/alpha-D-Glucose/name

91# m/z search in positive mode

92https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M%2BH/0.5

94# Exact mass search

95https://www.metabolomicsworkbench.org/rest/moverz/exactmass/PC(34:1)/M%2BH

96```

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

# Compounds with a formula (not unique chemical identity)
https://www.metabolomicsworkbench.org/rest/compound/formula/C6H12O6/all

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

# 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/MB/635.52/M%2BH/0.5

# Exact mass search
https://www.metabolomicsworkbench.org/rest/moverz/exactmass/PC(34:1)/M%2BH

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98## Response Format

99Most record queries default to JSON. `mwtab` returns MWTab text and `molfile` returns MOL text. `/moverz/exactmass/` returns a short HTML/text result: the live PC(34:1), M+H example returned 760.585077 and C42H83NO8P. No general pagination contract is exposed; keep queries narrow and inspect the actual content type and body. An HTTP 200 can contain an unsupported-input error. Resolve names through RefMet; `compound/name` is not a supported input item.

100

Response Format

Most record queries default to JSON. mwtab returns MWTab text and molfile returns MOL text. /moverz/exactmass/ returns a short HTML/text result: the live PC(34:1), M+H example returned 760.585077 and C42H83NO8P. No general pagination contract is exposed; keep queries narrow and inspect the actual content type and body. An HTTP 200 can contain an unsupported-input error. Resolve names through RefMet; compound/name is not a supported input item.

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101## Rate Limits

102No published limits. Be reasonable. Add 0.5-1s delay for batch calls.

103

104Official query builder and contract: https://www.metabolomicsworkbench.org/tools/mw_rest.php

Rate Limits

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

Official query builder and contract: https://www.metabolomicsworkbench.org/tools/mw_rest.php

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