Metabolomics WorkBench REST service

MW REST API (v1.0, 5/7/2019) Download API (pdf)

*Note: A number of new REST queries have been added that are not described in this API version (see new examples below)

The Metabolomics WorkBench REST service enables access to a variety of data (including metabolite structures, study metadata and experimental results) using HTTP requests. These requests may be carried out using a web browser or may be embedded in 3rd party applications or scripts to enable programmatic access. Most modern programming languages including PHP, Perl, Python, Java and Javascript have the capability to create HTTP request and interact with datasets such as this REST service.

The REST URL consists of three main parts, separated by forward slashes, after the common prefix specifying the invariant base URL:
(https://www.metabolomicsworkbench.org/rest/)

The context specification dictates which type of resource to access and is chosen from one of the following:
<study | sample | compound | refmet | gene | protein | moverz | exactmass>
The input specification is composed of 2 required parameters separated by forward slashes. The first parameter is the input item which depends on the context. The 2nd parameter is an appropriate input value for the chosen item. Examples of an input specification are:
/compound/pubchem_cid/311/
/compound/formula/C20H34O/
/study/study_id/ST000001/
/sample/mb_sample_id/SA002633/
/refmet/name/Cholesterol/
/refmet/match/LysoPC16:0/
/gene/gene_symbol/acaca/
/protein/uniprot_id/Q13085/
Exceptions to this input specification occur when the 'moverz' context (MS search) is selected. In this case the input value must consist of 3 parts separated by forward slashes: <m/z value>/<adduct>/<tolerance(Daltons)>, e.g. '635.52/M+H/0.2'. In the case of the 'exactmass' context the input value must consist of 2 parts separated by forward slashes: <lipid bulk abbreviation>/<adduct>, e.g. 'PC(34:1)/M+H' and the input and output items are ignored.
The output specification is composed of a required output item parameter and an optional output format parameter. The list of possible output items depends on the value chosen for the context. In the case of the "compound" context one or more (separated by commas) of 'regno', 'formula','exactmass', 'inchi_key', 'name', 'sys_name', 'smiles', 'lm_id', 'pubchem_cid', 'hmdb_id', 'kegg_id', 'chebi_id', 'metacyc_id' may be specified. More conveniently, an output type of 'all' may be specified to retrieve all compound-related fields. Also an output type of 'classification' retrieves the LIPID MAPS/ClassyFire classification hierarchy. In the case of the "study" context, allowed output types are 'summary', 'factors', 'analysis', 'metabolites' and 'data'. The default output format is JSON which is amenable to manipulation and parsing by various programming languages. Optionally a text ouput format may be specified, for example:
/compound/pubchem_cid/311/all/txt
Exceptions to this output specification occur when either 'molfile' (molfile is downloaded) or 'png' (png image is displayed in browser) is chosen as an output item in the "compound" context.

The interactive "REST url" creator below shows most of the currently available options for this service.

Base URL	/Context	/Input item	/Input value	/Output item	/Output format
https://www.metabolomicsworkbench.org/rest	/	/	/	/	/

(What is REST?) (What is JSON?)

The table below contains several examples of REST urls.

Example request	Example URL
Compound context
Fetch compound common name from Metabolomics Workbench database regno	https://www.metabolomicsworkbench.org/rest/compound/regno/11/name
Fetch all compound fields from Metabolomics Workbench database regno	https://www.metabolomicsworkbench.org/rest/compound/regno/11/all
Fetch all compound fields as text from Metabolomics Workbench database regno	https://www.metabolomicsworkbench.org/rest/compound/regno/11/all/txt
Fetch compound smiles from PubChem compound ID	https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/439577/smiles
Fetch compound common name and sytematic name from InChIKey	https://www.metabolomicsworkbench.org/rest/compound/inchi_key/JTWQQJDENGGSBJ-UHFFFAOYSA-N/name,sys_name
Fetch all compound fields from formula (multiple records)	https://www.metabolomicsworkbench.org/rest/compound/formula/C20H34O/all
Fetch compound classification hierarchy from PubChem compound ID	https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/classification
Download compound molfile from Metabolomics Workbench database regno	https://www.metabolomicsworkbench.org/rest/compound/regno/28606/molfile
Fetch png image of structure from Metabolomics Workbench database regno	https://www.metabolomicsworkbench.org/rest/compound/regno/11/png
Study context
Show all publicly available studies (Project, Study, Analysis ID)	https://www.metabolomicsworkbench.org/rest/study/study_id/ST/available
Fetch summary information for a study	https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary
Fetch samples and experimental variables (factors) for a study	https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors/
Fetch summary information for all studies	https://www.metabolomicsworkbench.org/rest/study/study_id/ST/summary
Fetch analysis information for a study	https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/analysis
Fetch metabolites and annotations detected in a study (one study at a time)	https://www.metabolomicsworkbench.org/rest/study/study_id/ST000009/metabolites
Fetch named metabolite measurements for a study (one study at a time)	https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data
Fetch mwTab content for an analysis within a study in mwTab format	https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000001/mwtab/txt
Fetch mwTab content for an analysis within a study in json format	https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000001/mwtab
Fetch species information (as text) for all studies	https://www.metabolomicsworkbench.org/rest/study/study_id/ST/species/txt
Fetch sample source information (as text) for all studies	https://www.metabolomicsworkbench.org/rest/study/study_id/ST/source/txt
Fetch disease association (where applicable) for all studies	https://www.metabolomicsworkbench.org/rest/study/study_id/ST/disease
Fetch list of studies with untargeted data in NMDR*New	https://www.metabolomicsworkbench.org/rest/study/study_id/x/untarg_studies/
Fetch untargeted data (where applicable) for an analysis within a study*New	https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000113/untarg_data/
Fetch experimental factors for an untargeted data analysis within a study*New	https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000113/untarg_factors/
Fetch list of studies with named metabolites in NMDR*New	https://www.metabolomicsworkbench.org/rest/study/study_id/ST/named_metabolites/
Show number of named metbolites in a study*New	https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/number_of_metabolites/
Fetch list of studies (as text) containing a RefMet name*New	https://www.metabolomicsworkbench.org/rest/study/refmet_name/Cholesterol/data/txt/
Fetch list of studies (as text) containing a KEGG_ID*New	https://www.metabolomicsworkbench.org/rest/study/kegg_id/C00002/data/txt/
Show metabolite name and RefMet name for a (NMDR) metabolite_id*New	https://www.metabolomicsworkbench.org/rest/study/metabolite_id/ME272191/available/
Fetch table of results (identified metabolites) for an analysis_id*New	https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000001/datatable/
Download table of results (identified metabolites) for an analysis_id*New	https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN000001/datatable/file
Show raw data files and size (in bytes) for a study_id*New	https://www.metabolomicsworkbench.org/rest/study/study_id/ST002082/rawdatasize
Sample context
Fetch information for an individual sample in a study*New	https://www.metabolomicsworkbench.org/rest/sample/mb_sample_id/SA002633/all
RefMet context
Fetch all RefMet fields from name	https://www.metabolomicsworkbench.org/rest/refmet/name/Cholesterol/all
Fetch all RefMet fields from formula	https://www.metabolomicsworkbench.org/rest/refmet/formula/C12H24O2/all
Standardize metabolite name or PubChem/KEGG/HMDB/ChEBI/LIPID MAPS identifier to RefMet*New	https://www.metabolomicsworkbench.org/rest/refmet/match/citrate/name/
Fetch entire RefMet database (Name,exact mass,formula,InChIKey,PubChemID,classification)*New	https://www.metabolomicsworkbench.org/rest/refmet/all
Fetch all RefMet names*New	https://www.metabolomicsworkbench.org/rest/refmet/name
Fetch all RefMet names and chemical classification*New	https://www.metabolomicsworkbench.org/rest/refmet/classification
Gene/protein context
Fetch all gene fields from gene symbol	https://www.metabolomicsworkbench.org/rest/gene/gene_symbol/acaca/all
Fetch gene name from Entrez gene id	https://www.metabolomicsworkbench.org/rest/gene/gene_id/31/gene_name
Fetch all protein fields from UniProt id	https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/all
Fetch all protein fields from Entrez gene id	https://www.metabolomicsworkbench.org/rest/protein/gene_id/19/all/
Fetch mRNA id from protein Refseq id	https://www.metabolomicsworkbench.org/rest/protein/refseq_id/NP_005493/mrna_id/
Mass spectrometry context
Perform MS precursor ion search on Metabolomics Workbench database with m/z 635.52, ion-type* M+H and mass tolerance of 0.5 and output as text	https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M+H/0.5/txt
Perform MS precursor ion search on LIPIDS virtual database with m/z 513.45, ion-type* M-2H (2-) and mass tolerance of 0.2 and output as text	https://www.metabolomicsworkbench.org/rest/moverz/LIPIDS/513.45/M-2H/0.2/txt
Perform MS precursor ion search on RefMet database with m/z 255.2, ion-type* M+H and mass tolerance of 0.2 and output as text	https://www.metabolomicsworkbench.org/rest/moverz/REFMET/255.2/M+H/0.2/txt
Calculate the exact mass (m/z) of the [M+H]+ ion of the lipid abbreviation# PC(34:1)	https://www.metabolomicsworkbench.org/rest/exactmass/PC(34:1)/M+H

*Ion-types:
Positive: M+H, M+2H, M+3H, M+4H, M+H-H2O, M+H-Hexose, M+H-EtnP, M+H-SerP, M+H+CH3OH, M+H+CH3CN, M+H+2CH3CN, M+Na+CH3CN, M+NH4, M+Ag, M+Na, M+2Na-H, M+2K-H, M+2Na, M+K, M+2K, M+Li, M+2Li, M.NaFormate-H, M.NaFormate+H, M.NH4Formate-H, M.NH4Formate+H, M., M.CH3
Negative: M-H, M-2H, M-3H, M-4H, M-CH3, M-H-H2O, M.Cl, M.F, M.HF2, M.OAc, M.Formate, M.NaFormate-H, M.KFormate-H, M+Na-2H, M+K-2H, M-H-Ser
Uncharged: Neutral

#Lipid abbreviations:
FA, CoA, CAR, MG, DG, TG, PA, PC, PS, PE, PG, PGP, PI, PIP, PIP2, PIP3, MGDG, DGDG, SQDG, Cer, SM, CerP, PE-Cer, PI-Cer, GlcCer, GalCer, LacCer, GM3Cer, GM4Cer, GB3Cer, iGB3Cer, asialo-GM2Cer, Lc3Cer, Manb1-4GlcCer, MolluCer, ArthroCer, CE
Lipid abbreviation notes: These are sum-composition or "bulk" abbreviations (<total number of carbons in chain(s)>:<total number of double bonds in chain(s)>). Sphingolipid abbreviations must contain a letter prefix indicating number of hydroxyl groups (<m|d|t>), for example, Cer(d34:1) for a ceramide, Cer(t32:0) for a phytoceramide and Cer(m32:1) for a 1-deoxyceramide.

REST (REpresentational State Transfer) is an architectural style consisting of a coordinated set of architectural constraints applied to components, connectors, and data elements, within a distributed hypermedia system. REST ignores the details of component implementation and protocol syntax in order to focus on the roles of components, the constraints upon their interaction with other components, and their interpretation of significant data elements.
Fielding, Roy T. (2000). "Chapter 5: Representational State Transfer (REST)". Architectural Styles and the Design of Network-based Software Architectures (Ph.D.). University of California, Irvine.
Fielding, Roy T.; Taylor, Richard N. (May 2002), "Principled Design of the Modern Web Architecture" (PDF), ACM Transactions on Internet Technology (TOIT) (New York: Association for Computing Machinery) 2 (2): 115-150, doi:10.1145/514183.514185, ISSN 1533-5399
REST Wikipedia page

JSON (JavaScript Object Notation) is a lightweight data-interchange format which human readable and also convenient for computers to parse and generate. JSON is a text format that is completely language independent but uses conventions that are familiar to most common programming languages.
Official JSON website