• National Metabolomics Data Repository

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    As of 10/21/20 the National Metabolomics Data Repository (NMDR) contains 1256 publicly available studies.
    A total of 1436 studies have been processed by the NMDR and the remainder (180) will be made available subject to their embargo dates.

    Recently released studies on NMDR

    ST001495 - Effects of Synbiotic Administration on Fecal Microbiome and Metabolomic Profiles of Dogs receiving Antibiotics; Canis familiaris; University of California, Davis

    ST001494 - Metabolomics of murine embryos cultured in a microfluidic device and comparison with traditional microdrops culture; Mus musculus; University of Leeds

    ST001493 - Dynamic binning peak detection and assessment of various lipidomics liquid chromatography-mass spectrometry pre-processing platforms; Homo sapiens; University of Groningen, Netherlands

  • Exemplary Studies

    A list of exemplary studies are listed here which adhere to the submission guidelines of Metabolomics Workbench. Specifically, publically available studies having all or most of the features below were identified as exemplary studies.

    • Well-written study summary
    • Detailed metadata for collection/treatment/chromatography/MS/NMR, etc.
    • Post-processing details
    • Presence of control samples
    • Raw data availability for samples and controls
    • One-to-one mapping of sample names to raw data file name
    • Internal standards (with measurements)
    • Clear and organized metabolite annotations

    These include different analysis (GC-MS, LC-MS, NMR) and species type. We recommend looking at these studies as a model example before submitting to Metabolomics Workbench.

  • Highlights

    August, 2020

    Metabolomics Workbench Metabolite Database: The Metabolomics Workbench Metabolite Database contains structures and annotations of biologically relevant metabolites. As of August, 2020, the database contains about 136,000 entries, collected from public sources such as LIPID MAPS, ChEBI, HMDB, PubChem, NP Atlas , CHEMBL and KEGG. The Metabolite Database is integrated with the NMDR data repository, providing links to studies reporting each metabolite. It is also integrated with the RefMet standardized reference nomenclature, providing structural information to metabolite species where applicable.

    LION/Web LION Enrichment analysis collaboration with NMDR:
    The Metabolomics Workbench is collaborating with LION/Web (http://www.lipidontology.com) to provide an efficient way to perform ontology enrichment analysis on lipidomics data contained in NMDR studies. LION/Web has incorporated a a REST service into their online application to enable users to specify an NMDR study id of interest which extracts the relevant metabolomics data/metadata from the NMDR repository where it can then be manipulated in the LION/Web enrichment analysis workflow.

  • Metabolomics News


    • Jupyter Notebooks has been released to analyze studies

      Analysis of all the studies in Metabolomics workbench can now be done by launching Jupyter Notebooks The notebooks can be launched at Binder. Alternatively, you may download notebooks from Github repository.

    • Individual mwTab file for all studies can now be viewed and downloaded as JSON format.

    news archive

NIH Common Fund Stage 2 Metabolomics Consortium Centers
Metabolomics Consortium Coordinating Center (M3C)
Richard Yost, U. of Florida
Metabolomics Workbench/NMDR
Shankar Subramaniam, UC San Diego
(this website)
Compound Identification Cores (CIDCs)
Arthur Edison, U. of Georgia
Alexey Nesvizhskii, U. of Michigan
Oliver Fiehn, UC Davis
Dean Paul Jones, Emory University
Thomas Metz, Pacific Northwest Nat. Lab.
Data and Tools Cores (DTCs)
John Weinstein, MD Anderson Cancer C.
Jamey Young, Vanderbilt University
Xiuxia Du, U. of North Carolina Charlotte
Shuzhao Li, Emory University
Alla Karnovsky, U. of Michigan
Katerina Kechris, U. of Colorado, Denver
Gary Patti, Washington U. at St. Louis

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