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


Request for Applications: Pilot and Feasibility Projects

The Metabolomics Consortium Coordinating Center (M3C) together with the Southeast Center for Integrated Metabolomics (SECIM) requests applications for up to 12-month pilot projects.

The goal of the NIH Common Fund’s Metabolomics program (see 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.  In order to catalyze science around the role of metabolomics in human health, the Metabolomics program supports research to establish a long standing national public repository for metabolomic data, to overcome technical hurdles in analyzing and interpreting metabolomics data, including the ability to determine metabolite identities, and to develop best practices and guidelines with help from the national and international metabolomics communities to promote accuracy, reproducibility, and re-analysis of metabolomics data. 

Specific objectives of the current phase of the NIH Metabolomics Program include: (1) establishment of a National Metabolomics Data Repository (NMDR) which is widely adopted by the national and international metabolomics community, supports facile data and metadata deposition and access for re-use, and provides a means for citing the data and its provenance; (2) addressing key challenges in analyzing and interpreting metabolomics data by catalyzing the field of compound identification to dramatically increase the number of identified biomedically-relevant, metabolites in metabolomics spectra; (3) addressing key challenges in analyzing and interpreting metabolomics data by developing novel tools to facilitate metabolomics data analysis and interpretation; and (4) community engagement and program coordination to generate consensus and achieve wide-spread adoption of standards and guidelines for best-practices and data sharing in metabolomics.

M3C is the Metabolomics Consortium Coordinating Center of the NIH Common Fund’s Metabolomics program; the mission of the M3C is to serve as a catalyst for the advancement of metabolomics in biomedical research and clinical care by engaging the diverse range of stakeholders, organizing the consortium, and promoting its work. Stakeholder engagement includes symposia to identify roadblocks in the use of metabolomics and suggest approaches leading to remediation. Pilot and Feasibility awards focus on biomedical research projects new to the use of metabolomics.  Consortium work is organized through a web portal (see, providing access to all consortium resources, including access to datasets in the National Metabolomics Data Repository, and tools developed by the Metabolomics Data Analysis and Interpretation Tools awardees.  M3C further organizes the work of the consortium by facilitating on-line and in-person meetings of governance groups and workgroups.  M3C promotes the work of the consortium through social media (@metabinfo), its web portal, presentations at scientific meetings, and distribution of consortium standards, policies, procedures, protocols, best practices, and guidelines. The work of the coordinating center, and of the metabolomics consortium, will lead to improved human health through basic research findings, improved laboratory practices, and translation to clinical research and care.

The Southeast Center for Integrated Metabolomics at the University of Florida (SECIM, see was established in the first phase of the Common Fund’s Metabolomics program, and continues to provide world-class metabolomics services and research through UF’s Clinical and Translational Sciences Institute, as well as serving as the home of M3C. Pilot and Feasibility Awards are intended to support projects that will provide preliminary data for new extramural grant application submissions. The review process will emphasize innovation and the potential of the work to have a significant impact on an important biomedical research problem.


The overarching goal of the M3C will be the promotion of metabolomics as a key component of biomedical research (basic, clinical, and translational) and clinical care. The Pilot and Feasibility Program is a part of stakeholder engagement meant to enhance metabolomics research by providing support for investigators new to the metabolomics field, the development of new teams and partnerships, and high-risk/high-impact research. This program will focus on awards for the generation of metabolomic data from samples in biomedical research where previous work is rare or nonexistent. The program also aims to open additional areas of biomedical research to the use of metabolomics by specifically inviting biomedical researchers to apply. The Pilot and Feasibility Program aims to form new multidisciplinary collaborations that will enhance the integration of new techniques that benefit multiple investigators; it also aims to promote the consortium objectives (compound identification and data analysis). Applications from basic, translational, and clinical researchers are encouraged. Extending the collaborative nature of research projects by matching funds from other mechanisms is encouraged.


All basic, translational, or clinical investigators located at institutions within the United States who are eligible to apply as a PI for NIH grants are welcome to apply for M3C pilot awards. Young investigators and investigators who are new to the field of metabolomics are especially encouraged to apply.

Application Procedure

Applications should be submitted using the instructions that can be found on the M3C’s website ( PHS 398 format is required.  Deadline date for receipt is Friday, April 16, 2021.  NIH application guidelines will be followed.

Applications must include the following elements:

  • Cover Sheet
  • Abstract
  • Budget and budget justification
  • NIH biographical sketches
  • Eligibility statement
  • Research Strategy (5 pages maximum) must include:   Specific Aims, Background, Significance, and Rationale for the use of metabolomics, Impact, Preliminary Results (if any), Experimental Approach
  • Plans for future funding
  • References
  • Protection of human and/or animal subjects

Additional Considerations

M3C is dedicated to funding as many unique and innovative projects as possible with goals of expanding the range of biomedical applications of metabolomics and advancing metabolomics technology in the identification of metabolites.  Impactful applications of $15,000 or less will typically receive preference over those with higher budgets. Requests for salary for the Principal Investigator or personnel, laboratory or extramural services outside of M3C are not permissible. All funds will be awarded in credit toward services performed at SECIM, including study design and some statistical support, or in payment for the project’s materials and supplies.

M3C specifically encourages applications that form scientific partnerships, span several scientific domains, include trainees, and benefit multiple investigators. The role of the PI, trainee(s), and collaborators affiliated with the project should be clearly defined. The names of all funded investigators will be posted on the M3C website. Grantees must acknowledge the M3C NIH grant U2CDK119889 in any abstracts, presentations, or publications resulting from supported studies and provide quarterly progress reports, a final report, and an annual report that includes publications and new grant awards. As mandated by the NIH Common Fund Metabolomics Program, all resulting metabolomics data and associated metadata will be publicly deposited in the National Metabolomics Data Repository (NMDR).

Application Review

All submitted applications will be internally reviewed by the M3C Steering Committee for technical feasibility and compliance with the above requirements and formats. External reviews will use the NIH review scoring criteria and scores. Final funding decisions will be made by the Metabolomics Program Executive Committee.

Application receipt deadline: April 16, 2021

Earliest funding start date: June 14, 2021

Interested investigators are encouraged to discuss their applications with SECIM Faculty:

Proposals must be submitted by no later than 5:00 p.m., April 16, 2021, to Dr. Alisha Mitchell-Roberts,

Application Instructions (docx file)

Application Forms

Abstract (docx format)

Budget (docx format)

Justification (docx format)

NIH Biographical Sketch (docx format)

Eligibility Statement (docx format)

Research Strategy (docx format)

Plans for Future Funding (docx format)

References (docx format)

Protection of Human and Animal Subjects (docx format)


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.