Upload and Manage Experimental Data and Metadata

The National Metabolomics Data Repository (NMDR) is now accepting metabolomics data for small and large studies on cells, tissues and organisms via the Metabolomics Workbench. We can accommodate a variety of metabolite analyses, including, but not limited to MS and NMR. In order to ensure reproducibility and interoperable use of data, we require experimental metadata (see tutorials) to be deposited along with the metabolite measurements. Processed data (measurements) maybe in the form of quantitated metabolite concentrations, MS peak height/area values, LC retention times, NMR binned areas, etc. Raw data in the form of MS and NMR binary files and associated parameter files may also be uploaded. We accept data from both targeted and untargeted studies. The Metabolomics Workbench also provides a suite of tools for analysis and visualization of the data. Step-by-step instructions for the whole process are provided below.

Requirements for depositing data via the Metabolomics Workbench:

  1. Register; check the box corresponding to "I wish to be authorized to upload data" '.
  2. E-mail us for authorization (help@metabolomicsworkbench.org).
    • We will contact you after we have reviewed your request for authorization to upload data (typically w/in 5 business days).
  3. Log in.
  4. View the list of exemplary studies (below) for examples of best practices for study submissions.
  5. The use of the common metabolite names in the RefMet database is strongly encouraged in order to be able to compare and contrast metabolite data across different experiments and studies. For your convenience an online tool is available to map your current metabolite identifications (where possible) to the corresponding RefMet names.
  6. Use the 'New Data Upload' tab to (a) register your study, (b) submit metadata and processed data and (c) upload raw data/supplementary material . (Please read the step-by-step tutorial). Please indicate the date when the study may be made available to the public.
  7. E-mail us for additional assistance (help@metabolomicsworkbench.org), if needed.

Raw data upload:
IMPORTANT! Please upload raw data in open-source format (mzML,mzXML,CDF) if at all possible to enable re-use and re-analysis. Compressed (zip, 7z, gz) data files are selected and uploaded to the NMDR FTP server through a FTP client. A variety of free and commercial standalone file transfer clients exist to upload large data files directly to the FTP servers: FileZilla, WinSCP, download managers, etc. The usage of FileZilla is recommended for uploading data to the NMDR.

List of 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.

Accessing and reviewing deposited data/metadata on the Metabolomics Workbench

After the NMDR has processed your dataset (typically less than 30 days), you will be notified and may review it at the following private website: http://dev.metabolomicsworkbench.org:22222/data/browse.php

In order to browse and review data and metadata from experimental projects and studies submitted by your institution (or other institutions for which you have permission to view), you will be prompted to login with your Metabolomics Workbench username and password. After you have reviewed your dataset and communicated with the NMDR, the study will be placed on the public Metabolomics Workbench website (subject to its embargo date, if any).

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