Frequently Asked Questions (FAQs)

1. What is the Common Fund Data Ecosystem (CFDE)?
The Common Fund Data Ecosystem (CFDE) is intended to provide the infrastructure needed to help solve key challenges facing Common Fund Data Coordinating Centers. CFDE will include a portal or central access point for Common Fund data sets, tools, and other digital objects, through which users can access and compute on data in a cloud environment. This CFDE portal is not designed as a data repository or platform, but will instead link multiple data platforms that have been established through Common Fund programs and create cloud workspaces for users to access and compute on data across the different platforms. While users may continue to access an individual data set via the platform created for that data set, the CFDE will foster new discoveries and support different types of analyses by enabling queries of multiple data sets simultaneously. The CFDE will provide user support through automated help tools, online courses, webinars, and in-person training events. By providing infrastructure, advice, resources, best practices, common components, and services to fit the needs of Common Fund programs, the CFDE will increase the utility of Common Fund digital objects by making them more findable, accessible, interoperable, and reusable, also known as FAIR. The CFDE will require a collaborative effort, involving Common Fund Data Coordinating Centers who represent the data generators for each program, and a central coordinating component known as the CFDE Coordinating Center (CFDE-CC).

See an overview presentation of the CFDE concept at the September 2019 Council of Councils meeting, and watch the animated Overview of the Common Fund Data Ecosystem video to learn more.

2. Why is the CFDE focused on Common Fund (CF) data sets? Isn’t there a need for NIH to tackle this issue as a whole?
The NIH recognizes a need to modernize the NIH-funded biomedical data science ecosystem. The NIH Office of Data Science Strategy (ODSS), located within the Office of the Director, provides leadership and coordination on a broad range of NIH-wide data science activities to realize NIH’s vision for a modernized and integrated biomedical data ecosystem. ODSS is working across NIH to share information, adopt best practices, and leverage lessons learned from similar efforts, including the CFDE. As ODSS is responsible for NIH-wide data science efforts, the CFDE is focused on making Common Fund data more usable and useful to maximize the impact of Common Fund-supported programs. This focus aligns with the concept approved by the NIH Council of Councils to establish the CFDE as an infrastructure investment for Common Fund data sets. However, Common Fund programs are intended to create data sets that are useful to a very broad community. Common Fund data sets are usually related to other data sets supported by NIH Institutes/Centers or other entities. They may share data types or user communities such that a given user may want to access Common Fund data and non-Common Fund data together. The CFDE is working to create technology to prepare for a future of data sharing with other data ecosystems internal or external to the NIH. Participating Common Fund Data Coordinating Centers are invited to include collaborations with related data sets/platforms as they engage with the CFDE.

For more details on NIH-wide efforts, please see the NIH Strategic Plan for Data Science.

3. How is the Common Fund coordinating with ODSS or other NIH entities on these efforts?
NIH Office of Data Science Strategy (ODSS) located within the Office of the Director, provides leadership and coordination on a broad range of NIH-wide data science activities to realize NIH’s vision for a modernized and integrated biomedical data ecosystem. ODSS is working across NIH to share information, adopt best practices, and leverage lessons learned from similar efforts, including the CFDE. As ODSS develops solutions for trans-NIH data challenges, such as the need for single sign-on to access multiple data sets, the CFDE will pilot the solutions, provide feedback, and ultimately adopt standard approaches.

The Common Fund participates in the ODSS Technical Implementation Working Group and is also working with ICs to develop and demonstrate interoperability across data platforms. The Common Fund recognizes the importance of coordination across NIH to achieve long-term goals and will continue to align with these other efforts.

4. What types of data will be accessible via the CFDE?
Common Fund programs produce a wide variety of data types, including but not limited to genomic, epigenomic, transcriptomic, proteomic, metabolomic, imaging, and clinical data. The data and tools for each program are stored, managed, and made available through that program’s Data Coordinating Center or equivalent. The data include both raw and processed data, along with associated metadata and tools. The CFDE will not replicate or otherwise serve as a repository for these data sets; it will instead work with the individual program Data Coordinating Centers to provide access to the data through the CFDE portal as a way for users to gain access to multiple data sets simultaneously.

Since individual Common Fund programs are supported for a maximum of ten years, the CFDE will support ongoing data storage and maintenance costs so that data from programs that have ended continue to be accessible.

5. What about CF data/tools once a Common Fund program ends?
The Common Fund is committed to ensuring that data and resources developed by Common Fund programs are useful to the broad biomedical research community, and the CFDE is a key component for ensuring data resource sustainability. Through the CFDE, the Common Fund will explore ways to make existing tools and data sustainable and accessible. As support for individual Common Fund programs are designed to be time-limited investments, the Common Fund cannot commit to ongoing expansion of data sets or enhancement of tools once a program ends. However, the CFDE and Data Coordinating Centers will work collaboratively to facilitate sustainability and accessibility of program tools and data over the long-term.

6. Will the CFDE establish standards for the Data Coordinating Centers (DCCs) to follow and generate tools to share within the whole Common Fund community?
Efforts to harmonize across the CF DCCs will be a collaborative activity between the CFDE and DCCs. These activities will take the form of direct input from the DCCs; participation in workshops, site-visits, interviews; and standards development and testing. These efforts are being led by the CFDE Coordinating Center.

7. What is the CFDE Coordinating Center (CFDE-CC) doing?
The CFDE-CC is identifying opportunities to support data sets and resources developed by Common Fund programs. The CFDE-CC is currently developing:

• A portal for researchers to locate Common Fund data
• A dashboard to provide data owners and Program Leadership information about data use
• A standardized data manifest to facilitate searchability across data sets and data harmonization
• A set of training materials
• A number of standards and tools for assessing FAIRness of data assets

8. What is the DCC Engagement Opportunity Announcement (EOA) and what will the awards support?
Recognizing that active engagement by Data Coordinating Centers (or their equivalents) is essential for the creation of an ecosystem of data, the NIH Council of Councils cleared a concept for DCC Engagement Awards at their May 2019 meeting. The Engagement Opportunity Announcement (EOA) was released on January 29, 2020 and rolling submissions were accepted through May 2021. As of June 2021, EOA applications may be submitted only after consultation with the CFDE Program Team at CFDE@od.nih.gov. These awards are intended to provide flexible support to enable DCCs to collaborate with the CFDE-CC and with each other to work toward interoperability. The EOA will support collaborations among DCCs that establish the CFDE in any or all of the three key areas listed below:

• Area 1. Enabling access to, and computation across, multiple data sets in a cloud environment.
• Area 2. Facilitating set-up and ramp-down of Common Fund DCCs.
• Area 3. Enabling end-users to compute on data in the cloud.

Each DCC may not elect to participate in all three key areas however, each DCC is expected to actively collaborate with the CFDE-CC in Area 1. Since interoperability depends on the questions to be addressed by combining data sets, the DCCs will work together to identify the types of questions that users are likely to be interested in and will work with the CFDE to enable interoperability to ensure relevant queries are possible. The DCCs will also be asked to identify challenges that they face in making their data sets FAIR and will be supported to collaborate with the CFDE to solve those challenges. For DCCs of programs that are just beginning to generate data, the DCCs will be able to collaborate with the CFDE-CC to incorporate lessons learned from earlier DCCs, thereby lowering barriers to the creation of new data sets. For DCCs of programs that are coming to an end, the DCC will be able to collaborate with the CFDE-CC to ensure sustainability of the data generated through the program.

9. Is participation in CFDE required for Common Fund programs?
The CFDE is a key component in the Common Fund’s long-term strategy for the sustainability, availability, and utility of its data. While Common Fund programs are not required to be part of the CFDE, they are encouraged to work with the CFDE and utilize best practices and resources from the CFDE.

10. Could a non-Common Fund DCC participate in the CFDE?
The CFDE is designed to enhance utility of Common Fund programs. The Common Fund recognizes that there are significant opportunities for interoperability across the NIH and is actively working with several NIH Institutes and Centers to explore these opportunities. That said, many Common Fund datasets are highly related to non-Common Fund datasets. While the CFDE DCC Engagement Awards are available only to Common Fund DCCs, each Common Fund DCC may bring related datasets into the CFDE as collaborators. As new programs are created by the Common Fund, these programs may also be eligible to participate in the CFDE in the future. Prior to applying for the DCC Engagement Opportunity it is recommended that DCCs arrange a visit or virtual meeting with the CFDE Coordinating Center in order to communicate opportunities and challenges they may face. For guidance or questions regarding this process please email us at CFDE@od.nih.gov.

11. How do I become part of the CFDE?
The Engagement Opportunity Announcement (EOA) (OTA-20-005) includes a list of Common Fund programs that may participate, please contact the CFDE Program Team at CFDE@od.nih.gov to initiate CFDE engagements.

Common Fund Data Ecosystem (CFDE) Questions   Common Fund Data Ecosystem (CFDE) Questions

1. Will the due date for the second round of Engagement Opportunity Announcement proposals be extended due to COVID-19?
As of June 2021, applications for Engagement Opportunity Announcement (EOA) (OTA-20-005) may be submitted only after consultation with the CFDE Program Team (email: CFDE@od.nih.gov).

2. Has the new submissions process changed anything about the requirements, submission instructions, and review process for Detailed Engagement Plans?
The requirements, submission instructions, and review process for Engagement Opportunity Announcement (EOA) (OTA-20-005) remain the same as described in the original EOA, with the following exceptions:

• As of June 2021, applications may be submitted only after consultation with the CFDE Program Team (email: CFDE@od.nih.gov).
• Proposed partnering activities with other DCCs should be described as tentative plans, pending delivery of a detailed description of activities, milestones, timeline, and budget to be developed in collaboration with partner DCC(s) post-award. Applicant DCCs should reach out to potential partner DCCs during the development of their Detailed Engagement Plans to gauge their interest in proposed joint activities.
• Unless otherwise approved by NIH Common Fund staff in advance, initial proposed budgets should only include support for efforts to engage with the CFDE-CC and to develop detailed collaboration plans with DCC partners. Budgets for proposed DCC-DCC collaborative activities will be discussed with NIH as part of the detailed collaboration plans developed post-award. Once plans for DCC-DCC collaborative activities are established, support for these activities will be provided.
• Budgets may be submitted in any format as long as they address the requested information described in OTA-20-005. Proposers may want to use this recommended budget format. Budgets can be uploaded as a separate attachment and do not count against the page limit.
• Starting in Year 2, budgets should include travel for a yearly CFDE meeting, at least 2 different consortium sites for information exchange, 2 training workshops, and 1 cross-pollination workshop.
• Review discussions of the Detailed Plans will take place via video-conference, and will include the PI(s) from the applicant DCC and key personnel (up to a total of 4 individuals), the CFDE-CC PI and Training Director, relevant NIH staff, and external experts. Proposed partnering DCC PIs will not need to participate in the review discussion.
• Detailed Plan review discussions are expected to occur within 1 month of receiving the Detailed Plans.
• Following the Detailed Plan review discussion, NIH anticipates initiating Other Transaction award negotiations within 2 weeks, and issuing awards within 5 weeks.

3. When will funds for the DCC Engagement Opportunity Announcement (EOA) be awarded, how much will they be, for how long, and how many awards?
The current budget for this effort is planned for approximately $7.5 million over a 3-year period for up to 13 awards. However, NIH Common Fund procedures and OT mechanisms allow for significant flexibility to make adjustments necessary to pursue catalytic and transformative initiatives. Award levels may increase or decrease over time based on programmatic needs, funding availability, and recipient performance.

4. May DCCs submit multiple applications?
No, only one proposal will be accepted per program. Individual DCCs within the same program should collaborate on a single proposal in order to qualify for review. If a DCC within a program has already received an award, a supplement request could be submitted through that awardee to expand collaborations. Also refer to the last question below.

5. When submitting the EOA, what budget format should be used?
Budgets may be submitted in any format as long as they address the requested information from the Engagement Opportunity Announcement (EOA) (OTA-20-005) (see Budget Details section, page 13). A recommended (not required) format for the budget can be found at: https://grants.nih.gov/grants/how-to-apply-application-guide/forms-e/gen.... Budgets can be uploaded as a separate attachment. Budgets to not count against the page limit.

6. The EOA says that there will be an additional cross-pollination workshop for the second round of engagements, with the date to be determined. Will there be a second workshop?
No, the second workshop has been canceled.

7. After the first round of proposals, if a DCC without an existing EOA wants to propose a collaboration with a DCC that received an EOA in the first round, does the DCC that already has an award need to submit an additional proposal?
No. After the first round of proposals, NIH only expects proposals from DCCs that do NOT already have an existing Engagement Opportunity Award. If new collaborative activities between a DCC with an existing award and a DCC submitting a new proposal are approved, the relevant existing DCC award can be modified to add the new collaborative activities.

CFDE Engagement Opportunity Announcement (OTA-20-005) Questions   CFDE Engagement Opportunity Announcement (OTA-20-005) Questions 

General FAQs

1. What kind of research falls under this RFA (RFA-RM-22-007)?
The submission of small research (R03) applications is encouraged from institutions and organizations proposing projects that lead to enhanced use of selected Common Fund data sets by the wider scientific community. Small research (R03) grants provide flexibility for initiating discrete, well-defined projects that can be completed in one year and require only limited levels of funding. This program supports different types of projects including, but not limited to, the following:

• Conducting pilot or feasibility studies based on analyses across data sets of at least two Common Fund programs
• Building synthetic cohorts, combining, and comparing data sets
• Leveraging existing data across humans and model organisms for novel discovery
• Developing research methods or analytic tools to support data visualization, harmonization, and integration
• Curating and/or annotating information in the data sets
• Applying new artificial intelligence/machine learning/deep learning approaches for metadata harmonization to aid in data integration
• Developing new approaches and tools for simultaneous analysis of data residing on multiple platforms (e.g., data sets residing in two separate cloud platforms)
• Developing workflows and tools to automate data integration and interoperability

This Funding Opportunity Announcement will not accept applications proposing clinical trials.

2. Can my application propose to generate new data?
Yes, projects can propose to generate new preliminary or validation data. Examples include (but are not limited to):

• Investigation of gene expression, genome topology, protein expression, and/or epigenetic patterns across several disease conditions, phases of the lifespan, or in analysis of sexual dimorphism Identification of biomarkers (metabolites, genetic variants, DNA methylation and/or histone marks) associated with various diseases and risk factors
• New approaches for integrating and analyzing single cell data
• Machine learning and computational approaches to identify likely areas of the genome and genetic variations/mutations related to human diseases
• Network analysis across genetic variation, expression profiling, and/or GWAS data to reveal pathways associated with various diseases Incorporating machine learning and computational approaches to imaging data for data harmonization
• Enhancement of information in the data resources through the development of analytic tools, curation and annotation of existing data, or addition of phenotypic or clinical information 

3. Which Common Fund program data sets are eligible for funding?
The established Common Fund program data sets listed below are well-poised for increased community use. Applicants must propose to use at least two or more data sets from the following list, although they can propose to use other data sets (both NIH Common Fund data sets and other NIH data sets) as well. Integration across multiple data sets is required.

• 4DNucleome (4DN): Reference nucleomics and imaging data sets, including an expanding tool set for open data processing and visualization. Link to 4DN Web Portal.
• Extracellular RNA Communication (ExRNA): Catalog of exRNA molecules found in human biofluids like plasma, saliva, and urine; and potential exRNA biomarkers for diseases. Link to exRNA Research Portal.
• Gabriella Miller Kids First (Kids First): Data from whole-genome sequencing of cohorts with structural birth defects and/or susceptibility to childhood cancer, with associated phenotypic and clinical data. Link to Kids First Data Resource Center.
• Genotype-Tissue Expression (GTEx): Whole genome- and RNA sequence data from multiple human tissues to study tissue-specific gene expression and regulation, including tissue samples. Link to GTEx Portal.
• Glycoscience: A data integration and dissemination project for carbohydrate and glycoconjugate related data. Link to GlyGen.
• The Human BioMolecular Atlas Program (HuBMAP): An open and global platform to map healthy cells in the human body to determine how the relationships between cells can affect the health of an individual. Link to HuBMAP Consortium.
• Illuminating the Druggable Genome (IDG): Data on understudied druggable proteins, including mRNA and protein expression data, phenotype associations, bioactivity data, drug target interactions, disease links, and functional information. Link to IDG Consortium.
• Integrated Human Microbiome Project (iHMP): Microbiome, epigenomic, metabolomic, and phenotypic data for 3 cohorts. Link to iHMP.
• Knockout Mouse Phenotyping Program (KOMP2): Data from broad, standardized phenotyping of a genome-wide collection of mouse knockouts. Link to International Mouse Phenotyping Consortium (IMPC).
• Library of Integrated Network-based Cellular Signatures (LINCS): Molecular signatures that describe how different types of cells respond to a variety of agents that disrupt normal cellular function. Link to LINCS Consortium.
• Metabolomics: Metabolomics data and metadata from studies on cells, tissues, and organisms. Link to Metabolomics Workbench.
• Molecular Transducers of Physical Activity in Humans (MoTrPAC): Data contain assay-specific results, associated metadata, quality control reports, and animal phenotype data related to molecular transducers that underlie the effects of physical activity. Link to MoTrPAC Data Hub.
• Stimulating Peripheral Activity to Relieve Conditions (SPARC): Maps and tools to identify and influence therapeutic targets that exist within the neural circuitry of a wide range of organs and tissues. Link to SPARC Portal.

4. Can non-Common Fund data sets be included in the research strategy?
Data analyses proposed should utilize data sets from at least two Common Fund programs listed above (see question 5), and may include other NIH data sets, as long as the external data are currently accessible through a public controlled access database or can be shared through such a database. Integration across multiple Common Fund data sets is required. For proposals that aim to co-analyze Common Fund data with other genomic data sets that are currently accessible through an NIH-approved repository (e.g., dbGaP) or some other public controlled access database (e.g., European Genome-phenome Archive), applicants must describe the database through which the proposed data are accessible to the research community and the details of the data set, including any data use limitations based on the associated consent form. For proposals that aim to co-analyze Common Fund data with genomic datasets that are not currently accessible through an NIH-approved repository (e.g., dbGaP) or some other public controlled access database (e.g., European Genome-phenome Archive), applicants must describe their ability and willingness to submit the individual-level sequence data to an NIH-approved repository (e.g., dbGaP) and provide an associated Institutional Certification using the current NIH template (https://osp.od.nih.gov/scientific-sharing/institutional-certifications/). If the Institutional Certification is not available, provide a Provisional Certification and describe the anticipated data use limitations and associated modifiers separately. If submitting a Provisional Certification with the application, please note that a completed Institutional Certification may be required prior to award.

5. Is there a minimum number of data sets that are required to be used?
Yes, applicants must propose to use at least two Common Fund data sets. In addition, these data sets must be from at least two of the Common Fund programs listed in the FOA (RFA-RM-22-007).

6. Where can I find more information about previously funded studies through the Notice of Special Interest: Availability of Administrative Supplements for Enhancing Utility and Usage of Common Fund Data sets?
More information on the administrative supplements funded through this NOSI can be found on the Funded Research webpage.

Application FAQs

7. Can an institution/research team submit more than one application to the RFA?

• Yes, there is no prohibition on the number of applications an institution may submit, provided the applications are scientifically distinct.
• Program Directors/Principal Investigators (PDs/PIs) and key personnel of the Data Coordinating Centers (DCCs) of the Common Fund programs, and researchers who are involved in the DCC activities as senior/key investigators are not eligible to respond to this announcement. Applicants who are not sure about their eligibility are strongly encouraged to contact the Program Officers listed in the program announcement to discuss their situation.

8. What are the details for funding levels?

• The Common Fund intends to commit approximately $2,000,000 in FY 2022. The number of awards is contingent upon NIH appropriations and the submission of a sufficient number of meritorious applications. Anticipated award amounts are for $200,000 in direct costs, which is larger than typical R03 grants. More information on the R03 funding mechanism can be found at https://grants.nih.gov/grants/funding/r03.htm.
• The project period for an application submitted under this FOA is one year.
• If experimental approaches are proposed, expense of the associated research activities should be limited to 20% of the project budget.

9. Do I need a letter of intent?

No, a letter of intent is not required.

10. What are the page limitations?

The research strategy of the application is limited to 6 pages. All other page limitations described in the SF424 Application Guide and the Table of Page Limits must be followed.

11. Are Non-Domestic entities and foreign components allowed to apply?

• Non-domestic entities and non-domestic components of U.S. organizations are not eligible to apply.
• Foreign components, as defined in the NIH Grants Policy Statement, are eligible to apply.

12. What are the requirements for data and resource sharing for this RFA?

All applications, regardless of the amount of direct costs requested for any one year, should include a Data and Resource Sharing Plan. The Data and Resource Sharing Plan will be considered during peer review and by program staff as award decisions are being made as appropriate and consistent with achieving the goals of the program.

13. How will applications be reviewed?

Applications will be evaluated for scientific and technical merit by an appropriate Scientific Review Group(s) convened by the Center for Scientific Review (CSR), NIH. Following initial peer review, recommended applications will receive a second level of review by the appropriate national Advisory Council or Board. The following will be considered in making funding decisions:

• Scientific and technical merit of the proposed project as determined by scientific peer review
• Availability of funds
• Relevance of the proposed project to program priorities

The R03 small grant supports discrete, well-defined projects that realistically can be completed in one year and that require limited levels of funding. Because the research project usually is limited, an R03 grant application may not contain extensive detail or discussion. Accordingly, reviewers should evaluate the conceptual framework and general approach to the problem. Appropriate justification for the proposed work can be provided through literature citations, data from other sources, from investigator-generated data. Preliminary data are not required, particularly in applications proposing pilot or feasibility studies.

Pilot Projects Enhancing Utility and Usage of Common Fund Data Sets (R03 Clinical Trial Not Allowed)  Questions Pilot Projects Enhancing Utility and Usage of Common Fund Data Sets (R03 Clinical Trial Not Allowed)  Questions