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Metabolomics Workbench specifications


Unique identifier OMICS_10271
Name Metabolomics Workbench
Restrictions to use None
Maintained Yes


  • person_outline Shankar Subramaniam

Publication for Metabolomics Workbench

Metabolomics Workbench citations


When Transcriptomics and Metabolomics Work Hand in Hand: A Case Study Characterizing Plant CDF Transcription Factors

PMCID: 5876533
PMID: 29495643
DOI: 10.3390/ht7010007

[…] advice on good laboratory practices in this regard [,,,]. Since the formation of the Metabolomics Standards Initiative (MSI) in 2005, a number of metabolomics data repositories, such as MetaboLights, Metabolomics Workbench, Metabolomics Repository Bordeaux (MeRy-B), or the Metabolic Phenotype Database (MetaPhen) have been developed [,,,,]. Those databases represent a rich resource of data, in part […]


A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

PMCID: 5808091
PMID: 29479297
DOI: 10.1007/s11306-017-1309-5

[…] MetabolomeXchange ( and > 1300 on OmicsDI (Perez-Riverol et al. ). These studies with data publicly available in dedicated repositories [MetaboLights (Haug et al. ), Metabolomics Workbench (Sud et al. ), MetaPhen (Carroll et al. ), MeRy-B (Ferry-Dumazet et al. ) and GNPS (Wang et al. )], directly link to 368 unique journal articles (as of 15th September 2017). 45. […]


Guidelines for Genome Scale Analysis of Biological Rhythms

J Biol Rhythms
PMCID: 5692188
PMID: 29098954
DOI: 10.1177/0748730417728663

[…] typically deposited in the European Bioinformatics Institute (EMBL-EBI) proteomics database: PRoteomics IDEntifications (PRIDE). Metabolomic data are typically deposited in MetaboLights (EBI) or the Metabolomics Workbench (UCSD). Circadian-specific data sets can also be deposited in CircadiOmics (). Similarly, it is recommended that authors upload all custom-built analytical methods to online rep […]


Elucidating the Structure of N1 Acetylisoputreanine: A Novel Polyamine Catabolite in Human Urine

PMCID: 5537715
PMID: 28782053
DOI: 10.1021/acsomega.7b00872

[…] re obtained using ACD/MS Fragmenter (Advanced Chemistry Development, Inc.; Toronto, ON, Canada).The MS/MS spectra for N1-acetylisoputreanine and N1-acetylisoputreanine-γ-lactam have been submitted to Metabolomics Workbench and will be submitted to METLIN and HMDB. […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] iments available. MassBase [] is a large repository providing raw and processed mass chromatograms on 46 398 samples of over 40 species, including several plants, analyzed by LC-MS, GC-MS, and CE-MS. Metabolomics Workbench [] is a repository of a variety of metabolomics experiments containing over 60 000 entries, including raw and processed MS data, a section with detailed protocols for the experi […]


Understanding the response to endurance exercise using a systems biology approach: combining blood metabolomics, transcriptomics and miRNomics in horses

BMC Genomics
PMCID: 5316211
PMID: 28212624
DOI: 10.1186/s12864-017-3571-3

[…] data is available at the NIH Common Fund’s Data Repository and Coordinating Center (supported by NIH grant, U01-DK097430) website,, where it has been assigned a Metabolomics Workbench Project ID: (UrqK1489). The data is directly accessible at: […]


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Metabolomics Workbench institution(s)
San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
Metabolomics Workbench funding source(s)
This work was supported by National Institute of Diabetes and Digestive and Kidney Diseases NIDDK of the National Institutes of Health under award number U01 DK097430–01.

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