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  • National Metabolomics Data Repository

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    As of 08/11/22 a total of 2174 studies have been processed by the National Metabolomics Data Repository (NMDR). There are 1883 publicly available studies and the remainder (291) will be made available subject to their embargo dates.

    Recently released studies on NMDR

    ST002235 - Application of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer; Homo sapiens; University of Texas MD Anderson Cancer Center

    ST002236 - The impact of IgE in gut and serum metabolomes in a murine experimental model of allergic enteritis; Mus musculus; Institute of Applied Molecular Medicine

    ST002232 - Steady-state metabolomics Saccharomyces cerevisiae mitochondrial fatty acid synthesis (mtFAS) mutants and CTP1 overexpression; Saccharomyces cerevisiae; University of Utah

  • Metabolite Structure Database

    Updates to the Metabolite Structure Database (February 2, 2022)

    The updated Metabolite structure database of primary and secondary metabolites at the Metabolomics Workbench contains new substructure and text-based searches including by chemical class. Over 164,000 structures have been added including over 10,000 sterols.

    Higlights/News archive

  • Correlated network graphs in NMDR

    Correlated network graphs using Debiased Sparse Partial Correlation (DSPC)

    The Metabolomics Workbench has released a new graphical tool for estimating and visualizing partial correlation networks in NMDR studies. It uses the Debiased Sparse Partial Correlation algorithm (DSPC) developed at U.Michigan. Nodes may be mapped to chemical classification or fold-change. Study example: See "Perform Network analysis on correlated metabolites" links here

    Higlights/News archive

  • 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.

  • NMDR studies and Jupyter Notebooks

    Analyze Workbench studies via Python-based Jupyter Notebooks. Launch notebooks on Binder or download notebooks from GitHub and run them locally.


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


Please cite:Metabolomics WorkbenchYou will get more info on how to cite here

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