Frequently Asked Questions (FAQs) about the NMDC

The NMDC was officially launched in 2019

The NMDC is 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

Visit our Community page to learn more about how researchers and organizations can collaborate with the NMDC

The NMDC closely coordinates with DOE user facilities and the NMDC Submission Portal and metadata standards are compliant with user facility metadata requirements. The NMDC will often work with user facility researchers to make their data available in the NMDC, and when submitting a user facility proposal, researchers can indicate their interest in working with the NMDC

  • ESS-DIVE is a primary data repository for environmental data generated through Department of Energy funding. 
  • NMDC EDGE is designed to run the NMDC standardized bioinformatic workflows and users cannot customize or change any tools or parameters, it is a point and click way to run the workflows that allows for researcher data to then be compared to data within the NMDC Data Portal that was processed using the exact same workflows. The workflows are also available to download locally for users that want to work in a command line environment. KBase is meant to be customizable in terms of the bioinformatics workflows, tools, and parameters that users can run.

The NMDC Submission Portal, Data Portal, and NMDC EDGE all 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

Email support@microbiomedata.org to discuss your specific circumstance with our metadata team

Our submission process still requires some manual 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

Currently, the NMDC offers metagenome, metatranscriptome, metaproteome, natural organic matter, and viruses & plasmids workflows that can be downloaded locally through our GitHub or Docker Hub, and they can all be run through NMDC EDGE. We will be releasing metabolome, lipidome, and long-read workflows in the near future. The NMDC does not offer an amplicon workflow, however other tools exist that can process amplicons in a standardized manner (e.g., QIIME 2). New tools, databases, and parameters are constantly being evaluated by our team to ensure that the NMDC remains up to date with the best microbiome data processing practices. The NMDC closely coordinates with the JGI and EMSL regarding workflow updates and new tools that can be implemented into the workflows. 

The metadata templates are available to download from the NMDC Submission Portal after inputting study information

Contact NMDC support (support@microbiomedata.org) to discuss options

Tutorials, videos, user guides and technical information are available from our Documentation site and within the products themselves (e.g., NMDC EDGE tutorials)

  • 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

Currently, the NMDC does not support human microbiome data, and is focused on diverse environmental microbiomes.

Email support@microbiomedata.org with clear details about your bug or issue. Please include any relevant screenshots of the problem so we can recreate the issue on our end. The team will put in a GitHub ticket for the problem to be resolved. If you would like a response, please indicate that in your email.

You may also submit general feedback about the NMDC products to this form.

Visit our User Research webpage to learn more about NMDC’s user-centered design, and to volunteer to contribute to user research efforts!

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