Data Use Policy
The National Microbiome Data Collaborative (NMDC), a new initiative aimed at empowering microbiome research, is gearing up its pilot phase after receiving $10 million from the U.S. Department of Energy (DOE) Office of Science. Spearheaded by Lawrence Berkeley National Laboratory (Berkeley Lab), in partnership with Los Alamos (LANL), Oak Ridge (ORNL), and Pacific Northwest (PNNL) national laboratories, the NMDC will leverage DOE’s existing data-science resources and high-performance computing systems to develop a framework that facilitates more efficient use of microbiome data for applications in energy, environment, health, and agriculture.
Nearly every ecosystem and organism on Earth hosts a diverse community of microorganisms – its microbiome. Yet we know little about the functions of individual microbes, let alone how they interact with each other, their hosts, or their environments, and how their activity varies over time or in response to perturbations. The past decade has seen tremendous advances in genome and metagenome DNA-sequencing technologies, which has led to an unprecedented volume of microbiome data being generated. However, further progress in the field has been hindered by the lack of computational infrastructure for processing and performing integrative analyses of these and other microbiome-relevant data.
The NMDC, led by the DOE Joint Genome Institute (JGI)’s Emiley Eloe-Fadrosh, will tackle this data integration challenge by developing a community-centric framework based on large-scale, collaborative partnerships that draw on the capabilities, expertise, and resources of four DOE national laboratories. The guiding principles at the initiative’s core are: making data findable, accessible, interoperable, and reusable (FAIR); connecting data and compute resources; and community engagement that supports open science and shared ownership.
“While this pilot project is led by DOE national labs, the data sets, resources, and community opportunities are open to all microbiome researchers, regardless of funding, institute, or domain,” said NMDC Deputy Lead and JGI Director Nigel Mouncey.
Capabilities not currently available to the microbiome research community that NMDC will enable include:
Part A: NMDC Data Contributor Checklist
- Discuss data archiving needs: data quantity, interaction of project data systems and personnel with NMDC, and formats with the NMDC team (firstname.lastname@example.org).
- Submit data in relevant community standards and apply QA/QC. (How will these standards be determined?)
- Organization of data and files
- Formats, naming, and units
- Flagging and data level designations
- Uncertainties in data values
- Provide data package documentation along with appropriate standardized metadata.
- Describe the contents of files and data in the files
- Provide clear descriptive data package title, abstract, keywords, authorship, and funding information
- Use consistent, descriptive file naming
- Provide raw data for long term preservation along with processed data (when appropriate)
- Document QA/QC performed
- Agree to the data contributor license below (Part B), and specify one of the standard NMDC data usage policies for serving data to the public. NMDC supports Creative Commons Attribution 4.0 License and the Creative Commons Public Domain Dedication for data usage rights. Metadata will always be available in the public domain, using the Creative Commons Public Domain Dedication. If you have data that cannot be released under a free, fair-use policy, contact email@example.com to discuss your options for archiving with NMDC.
- If you have data packages that combined will require on the order of 0.5TB or more storage or if packages individually will be on the order of 10 GB, please contact firstname.lastname@example.org in advance of storing your data.
Part B: UC Berkeley Lab Data Contributor License Agreement
In order to clarify the intellectual property rights granted with respect to any contributions from any person or entity (“Contribution“), The Regents of the University of California, Department of Energy contract-operators of the Ernest Orlando Lawrence Berkeley National Laboratory (“Berkeley Lab”) must have a Contributor License Agreement (the “Agreement“) agreed to by each contributor. The license granted hereunder is for your protection as a contributor as well as for the protection of Berkeley Lab; it does not change your rights to use your own Contributions for any other purpose.
Either individuals or businesses, governmental or non-profit entities, including without limitation, all employees or agents acting on behalf of any such entity (an Entity), may submit Contributions to the National Microbiome Data Collaborative (NMDC) data project (the Data Project) under this Agreement. By clicking “I Agree”, you indicate that you are entering this Agreement on behalf of an Entity, you represent that you have the authority to bind such Entity to this Agreement, in which case, the terms “You” and “Your” shall refer to such Entity, as further defined below.
Please read this document carefully before agreeing to it, and print a copy for your records if required.
You accept and agree to the following terms and conditions for (i) all contributions that You may have previously submitted to the Data Project, unless otherwise governed by a written license agreement, and (ii) Your present and future Contributions submitted to the Data Project. Except for the licenses granted herein You reserve all right, title, and interest in and to Your Contributions.
“You” (or “Your”) shall mean the holder of intellectual property rights in the Contributions or the Entity authorized by such holder of intellectual property rights to enter into this Agreement with Berkeley Lab. For Entities, the Entity making a Contribution and all other Entities that control, are controlled by, or are under common control with that Entity are considered to be a single Contributor. For the purposes of this definition, “control” means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, (ii) the power to appoint a majority of the board of directors or other similar governing body of such entity, (iii) ownership of fifty percent (50%) or more of the outstanding voting shares of, or other voting equity interests in, such entity, or (iv) any other beneficial majority ownership of such entity.
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