FAQ

Data Deposition

• General
  • Q: When should I deposit my metadata and results?
    A: Please deposit your metadata and results at your earliest convenience. Your data will not be made publicly available before the date you indicate. For data generated with NIH Common Fund Metabolomics Program grant support, the release date is no later than the acceptance date of the initial publication from the data set as described in the terms of the NIH Common Fund Metabolomics Data Sharing Plan. The embargo time for data sharing, however, will expire one year from the end of the active grant even if no papers are published. In the case of grant renewal, the data sharing embargo time will expire with the end of the funding period for the renewed grant. For non-NIH Common Fund Metabolomics Program supported data, it is expected that the specified release date will be compliant with the terms of their funding source.
  • Q: Can I deposit my metadata templates before my results are available?
    A: Yes. Once you register your data set, you will be able to upload files via the corresponding "Datatrack ID", shown under the "List Data Uploads" tab. The list of registered data sets will be available anytime you log in.
  • Q: My dataset is extremely large. What is the best way for me to send it?
    A: You should be able to upload your data to the NMDR via the interface provided under Data | Upload and Manage Data. We have received uploads of well over 100GB via this mechanism, and currently support upload speeds of up to 100Gbit/sec, limited only by the capabilities of your local machine.
  • Q: What happens after I deposit my data?
    A: We will begin processing your file(s) shortly after they are deposited. Processing is typically complete w/in 30days, after which time we will notify you with instructions regarding how to find your data on the Metabolomics Workbench, and how to cite the data deposition in publications. These instructions will include the Project ID and Study ID that have been assigned to your data.
  • Q: I am working on a paper. Can I send my data, but wait until my paper is published before my data is posted?
    A: Your data will not be made publicly available before the date you indicate. For data generated with NIH Common Fund Metabolomics Program grant support, the release date is no later than the acceptance date of the initial publication from the data set as described in the terms of the NIH Common Fund Metabolomics Data Sharing Plan. The embargo time for data sharing, however, will expire one year from the end of the active grant even if no papers are published. In the case of grant renewal, the data sharing embargo time will expire with the end of the funding period for the renewed grant. For non-NIH Common Fund Metabolomics Program supported data, it is expected that the specified release date will be compliant with the terms of their funding source.
  • Q: What if I need to upload additional files?
    A: Should you need to upload additional files, you may do so by clicking "Data" | "Upload and Manage Data" | "List Data Uploads", then clicking the appropriate Datatrack ID. (You must log in in order to view your data uploads.)
• Data Types
  • Raw Data
    • NMR
      • Q: Should I send free induction decay (FID) or fourier transformed (FT) data?
        A: The NMDR will accept either FID or FT data as your raw/unprocessed NMR data.
  • Processed Data
    • General
      • Q: There are several steps in my processing protocol. Should I deposit the output from each step?
        A: No. Please deposit only the final result as your processed data set. We do, however, encourage you to deposit the protocol/scripts used for arriving at your processed result.
• Embargo Times
  • Q: When will my data appear on the Metabolomics Workbench?
    A: Your data will not be made publicly available before the date you indicate. For data generated with NIH Common Fund Metabolomics Program grant support, the release date is no later than the acceptance date of the initial publication from the data set as described in the terms of the NIH Common Fund Metabolomics Data Sharing Plan. The embargo time for data sharing, however, will expire one year from the end of the active grant even if no papers are published. In the case of grant renewal, the data sharing embargo time will expire with the end of the funding period for the renewed grant. For non-NIH Common Fund Metabolomics Program supported data, it is expected that the specified release date will be compliant with the terms of their funding source.
• Data Identification / Citation
  • Q: How do I cite data that I have deposited with the NMDR?
    A: After processing and curation of the data by the NMDR and deployment on the public website, your dataset will be assigned a URL with a project identifier in the form: https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=PRXXXXXX which will enable end-users to access metadata, processed data, analysis interfaces and raw data related to your submission. Depending on the complexity of the study, the data may be subdivided into different studies within that project.
    
    When data has already been deposited and a project ID has been assigned:

    When citing data in the Metabolomics Workbench's National Metabolomics Data Repository, please be sure to reference both the Project ID and Project DOI, both of which can be found on the Project Summary page. We suggest the following language.

    Citation Template

    This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org where it has been assigned Project ID (insert Project ID here). The data can be accessed directly via it's Project DOI: (insert Project DOI here). This work is supported by Metabolomics Workbench/National Metabolomics Data Repository (NMDR) (grant# U2C-DK119886), Common Fund Data Ecosystem (CFDE) (grant# 3OT2OD030544) and Metabolomics Consortium Coordinating Center (M3C) (grant# 1U2C-DK119889).
    
    Note: the format for creating a hyperlink to a Project using it's Project DOI is https://doi.org/(insert Project DOI here).

    Example using the Citation Template to Cite Project PR000001

    This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org where it has been assigned Project ID PR000001. The data can be accessed directly via it's Project DOI: 10.21228/M8159B. This work is supported by Metabolomics Workbench/National Metabolomics Data Repository (NMDR) (grant# U2C-DK119886), Common Fund Data Ecosystem (CFDE) (grant# 3OT2OD030544) and Metabolomics Consortium Coordinating Center (M3C) (grant# 1U2C-DK119889)..
    
    In this example, to create a hyperlink to Project PR000001 using it's Project DOI — 10.21228/M8159B — the correct URL is https://doi.org/10.21228/M8159B.

    Human Health Exposure Analysis Resource (HHEAR) Projects and Studies

    HHEAR resources are made possible by NIH funding and must be properly acknowledged. Please include the following in your manuscripts, posters and presentations:
    Research reported in this publication was supported by the National Institute of Environmental Health Sciences of the National Institutes of Health under Award Number U2CES026555. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

    Please see the project summary page for other publications related to the given data set, which may also be appropriate to cite. 

    When no project ID has been assigned:
    
    Please use the following language to cite data that has not been assigned a Project ID:
    

    The data obtained in this study will be accessible at the NIH Common Fund's NMDR (supported by NIH grant, U01-DK097430) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org.

  • Q: How do I cite someone else's data?
    A: Please use the following language to cite data downloaded from the Metabolomics Workbench:

    When citing data in the Metabolomics Workbench's National Metabolomics Data Repository, please be sure to reference both the Project ID and Project DOI, both of which can be found on the Project Summary page. We suggest the following language.

    Citation Template

    This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org where it has been assigned Project ID (insert Project ID here). The data can be accessed directly via it's Project DOI: (insert Project DOI here). This work is supported by Metabolomics Workbench/National Metabolomics Data Repository (NMDR) (grant# U2C-DK119886), Common Fund Data Ecosystem (CFDE) (grant# 3OT2OD030544) and Metabolomics Consortium Coordinating Center (M3C) (grant# 1U2C-DK119889).
    
    Note: the format for creating a hyperlink to a Project using it's Project DOI is https://doi.org/(insert Project DOI here).

    Example using the Citation Template to Cite Project PR000001

    This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org where it has been assigned Project ID PR000001. The data can be accessed directly via it's Project DOI: 10.21228/M8159B. This work is supported by Metabolomics Workbench/National Metabolomics Data Repository (NMDR) (grant# U2C-DK119886), Common Fund Data Ecosystem (CFDE) (grant# 3OT2OD030544) and Metabolomics Consortium Coordinating Center (M3C) (grant# 1U2C-DK119889)..
    
    In this example, to create a hyperlink to Project PR000001 using it's Project DOI — 10.21228/M8159B — the correct URL is https://doi.org/10.21228/M8159B.

    Human Health Exposure Analysis Resource (HHEAR) Projects and Studies

    HHEAR resources are made possible by NIH funding and must be properly acknowledged. Please include the following in your manuscripts, posters and presentations:
    Research reported in this publication was supported by the National Institute of Environmental Health Sciences of the National Institutes of Health under Award Number U2CES026555. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

    Please see the project summary page for other publications related to the given data set, which may also be appropriate to cite. 

    For how to cite the Metabolomics Workbench as a general resource, please see our How to Cite page.