NMDC FAQs
Frequently Asked Questions (FAQs) about the NMDC
1. What services will be maintained from the NMDC?
We expect that the DOE-BRIDGE team will maintain services for the Submission Portal and the Data Portal. We understand that there are many ongoing projects that rely on these services and if you have concerns or questions, please reach out to support@berdatacoalition.org.
2. How long will the Submission Portal and Data Portal be available?
We anticipate the DOE-BRIDGE team will support these services in the short-term. Any plans to change the portals will be communicated in advance to the community.
3. Will services to support programmatic access (e.g., Runtime and nmdc-client) continue?
We anticipate the DOE-BRIDGE team will support these services in the short-term. Updates on timelines will be communicated in advance to the community. Longer term, data will be available with DOE-BRIDGE services.
4. What will happen to the Microbiome Certificate Program?
The Microbiome Certificate Program was released in early 2026. Educators can freely access all materials through Zenodo to integrate into their existing coursework. In partnership with the American Society for Microbiology, the 12-module program will remain available in ASM’s Education Portal and individuals will receive a personalized certificate upon successful completion of the program. We are actively exploring ways to continue to support development activities to further this training. If you are interested in partnering or developing your own microbiome training programs, please explore KBase’s MICROnet program or reach out to Emiley Eloe-Fadrosh at the Joint Genome Institute (JGI).
5. How can I get help getting my external multi-omics data processed?
DOE-BRIDGE will continue to support external multi-omics microbiome data in the short-term. Starting with a submission is still the first step in this process, and DOE-BRIDGE will work with individual data contributors for data processing and sharing. Reach out to support@berdatacoalition.org for any questions or requests. We encourage you to leverage the KBase platform (www.kbase.us) for custom analysis of microbiome data.
6. Will submitting to NCBI as a data broker on behalf of users continue?
Functionality of brokering data to NCBI will persist in the short-term. DOE-BRIDGE will evaluate data brokering on a case-by-case basis. Reach out to support@berdatacoalition.org for any questions or requests.
The NMDC was officially launched in 2019.
The NMDC was funded by the US Department of Energy, Office of Science. Our full funding statement can be found on the About Us page.
NMDC Vision: To connect data, people, and ideas to advance microbiome innovation and discovery.
NMDC Mission: To support a FAIR microbiome data sharing network, through infrastructure, data standards, and community building, that addresses pressing challenges in environmental sciences.
No, the NMDC does not store raw omics data, however the NMDC Data Portal is referred to as a data discovery platform and it provides links to the raw data available in primary data repositories. The Data Portal does contain processed multi-omics data that has been run through the NMDC standardized bioinformatics workflows.
The NMDC closely coordinated with DOE user facilities and the NMDC Submission Portal and metadata standards were compliant with user facility metadata requirements. The NMDC previously worked with user facility researchers to make their data available in the NMDC.
The NMDC Submission Portal and Data Portal utilize ORCiD information as the login credentials, so you do not need to create an NMDC-specific account.
Yes, the NMDC metadata requirements are more stringent than many primary data repositories, and many of the fields are directly transferable to templates used by primary data repositories such as NCBI. We recommend checking the metadata requirements of any primary data repository before starting work to ensure all required metadata fields are collected.
Our submission process still requires verification to ensure that all metadata fields are properly captured, and submitted data must also be processed by the NMDC bioinformatics workflows prior to becoming available on the Data Portal.
Our Data Use Policy outlines how to cite the NMDC and the data within the NMDC Data Portal.
The NMDC Data Portal does not contain any embargoes and all data within the Data Portal is open and available for reuse applications.
The metadata templates are available to download from the NMDC Submission Portal after inputting study information.
- The NMDC Submission Portal allows users to upload their data to the NMDC Data Portal.
- Making your data available through the NMDC increases the citations of your datasets and their associated DOIs, it makes your microbiome data FAIR which is rapidly becoming an integral part of funding agency data management plans. It also allows for your data to be included in larger meta-analyses, modeling efforts, and ML/AI applications, and increases the overall visibility of your research.
There is a bulk download feature available in the Data Portal, and researchers can also utilize the NMDC API to download data.
The NMDC does not support human microbiome data, and was focused on environmental microbiomes.
Visit our User Research webpage to learn more about NMDC’s user-centered design process.
