NIH Common Fund for Metabolomics

The goal of the Common Fund’s Metabolomics program is to inform basic, translational, and clinical research. Metabolomics is the scientific study of the chemical reactions that occur in organisms, cells, or tissues. Each reaction produces small chemicals called metabolites, which play critical roles in keeping our cells healthy and functioning properly. As these different chemical reactions and the metabolites they produce are unique to every individual, by improving metabolomics methods and making them more accessible to different researchers it may allow for more personalized diagnosis of disease and treatment methods moving forward.


Metabolomics Workbench

The Metabolomics Common Fund’s National Metabolomics Data Repository(NMDR), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego, has developed the Metabolomics Workbench. The Metabolomics Workbench serves as a national and international repository for metabolomics data and metadata and provides analysis tools and access to metabolite standards, protocols, tutorials, training, and more.

The data and other resources developed by the Common Fund Metabolomics program are managed by the Data
Repository and Coordinating Center (DRCC) at the San Diego Supercomputer Center, University of California, San
Diego. The DRCC makes these materials publicly available through the Metabolomics Workbench website.


Omics Discovery Index

The Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics).

Most data in the Datatsets Discovery Index can be accessed programmatically using a RESTful API. The API implementation is based on the Spring Rest Framework. Web-browsable API The OmicsDI API is web browsable, which means that: The query results returned by the API are available in JSONformat and also XML. This ensures that they can be viewed by human and accessed programmatically by computer. The main RESTful API page provides a simple web-based user interface, which allows developers to familiarize themselves with the API and get a better sense of the OmicsDI data before writing a single line of code.

OmicsDI project has been developed on GitHub, you can check or contribute to our development here


Metabolomics Consortium Workgroups

Workgroups are the primary mechanism for creating deliverables within the Metabolomics Consortium. Anyone may propose a workgroup for any purpose. The Steering Committee will approve the formation of workgroups. Workgroups are created to undertake work with a clear purpose, a defined deliverable, and a stated deadline, thereby allowing collaborative work in a structured environment.


As the community grows, the diversity of the participants’ interests and expertise increases and concomitantly, the ability to manage the work done within the community becomes more complex.  It becomes difficult to track the work everyone is doing in the community to help avoid people unknowingly working on the same issue or at cross-purposes. There is also a desire to increase the visibility of work being undertaken by consortium members and to encourage greater community engagement.


The lightweight structure of workgroups is designed to increase the overall productivity of the consortium through systematic prioritization and management of work being done throughout our widely-distributed community. The structure is meant to assert the least possible overhead and is derived primarily from experiences and guidelines of virtual organizations such as the World Wide Web Consortium, the Research Data Alliance, and the Apache Software Foundation.

At any time, some workgroups will be forming based on the interests of consortium members, while others are active as organized by their members, while still others are wrapping up their work.  The workgroup approach supports all phases of the work:

  • Clarify purpose and deliverables of each workgroup
  • Through the Steering Committee, align workgroups with program goals
  • Through M3C, provide support and guidance to workgroups as needed
  • Increase the number of and visibility of community contributors and contributions to the Metabolomics Consortium
  • Ensure that work is getting done
  • Translate workgroup deliverables into consortium common practices

Workgroup Formation

Workgroups should form with minimal effort and emerge naturally from discussions and needs within the consortium. A workgroup must encourage participation from consortium and community members.

Workgroup proposals should typically be one page or less and must include:

  • Title of the proposed workgroup
  • Workgroup chair. Name and contact information for workgroup chair.
  • Purpose of the workgroup. Include brief background and rationale as needed.
  • Describe the deliverables of the workgroup.
  • State the finish date for creation of the deliverables.
  • Proposed workgroup members. Workgroup members must be from at least three different consortium member institutions, including the NMDR, M3C, and NIH Working Group. Additional members may be from any institutions, including those beyond the consortium.

Workgroup proposals will be reviewed and approved by the consortium Steering Committee.

Workgroups approved by the Steering Committee will have their approved proposals posted publicly on the M3C web site.

If you are considering forming a workgroup, please discuss your idea with the M3C.  Following discussion, please post your idea to asking for comments and members.  This helps keep the workgroup processes open and helps the consortium stay engaged with topics of interest to them.