NMDC
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

  1. Discuss data archiving needs: data quantity, interaction of project data systems and personnel with NMDC, and formats with the NMDC team (support@microbiomedata.org).
  2. 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
  3. 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
  4. 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 support@microbiomedata.org to discuss your options for archiving with NMDC.
  5. 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 support@microbiomedata.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.

1. Definitions.

“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.

“Contribution” shall mean any data or other content including any modifications or additions to any existing data or content (including metadata), that is or has been intentionally submitted by You to Berkeley Lab for inclusion in, or documentation of, Berkeley Lab. For the purposes of this definition, “submitted” means any form of electronic, verbal, or written communication sent to Berkeley Lab or its representatives, for the purpose of adding to, modifying, and/or improving the Work other than a communication that is conspicuously designated in writing by You as “Not a Contribution.” Data Project and Contributions are collectively referred to herein as the “Work“.

2. Grant of License.

You hereby grant, to Berkeley Lab and its agents, under either the terms of the Creative Commons Attribution 4.0 International License or the CC0 1.0 Universal Public Domain Dedication, as selected, all rights necessary to copy, store, redistribute, and share Your data, metadata, and any other content of Your Work, with the public in accordance with Section 2 (b) below.
Excluding data that Berkeley Lab, in its sole discretion feels is export controlled or contains personally identifiable information, Berkeley Lab hereby agrees to share Your Work with the public subject to the terms of the Creative Commons Attribution 4.0 International License or the CC0 1.0 Universal Public Domain Dedication, as selected when You submitted your data.

3. Representations and Warranties.

If You are entering into this Agreement as an individual, You represent and warrant that You are legally entitled to grant the above license. If Your employer(s) has intellectual property rights in the Contributions, You represent and warrant that You have received permission to make Contributions on behalf of that employer, that Your employer has waived such rights for Your Contributions to Berkeley Lab, or that Your employer has executed a separate contribution agreement with Berkeley Lab.

You represent and warrant that (i) You will observe all applicable United States and foreign laws and regulations (if any) with respect to the export, re-export, diversion or transfer of any software, any data, or both, including, without limitation, the International Traffic in Arms Regulations (ITAR) and the Export Administration Regulations, and (ii) You will not transfer to Berkeley Lab any personally identifiable information or any information that is export controlled other than information classified as EAR99 under the Export Administration Regulations without prior written authorization from Berkeley Lab.

If You are entering into this Agreement on behalf of an Entity, You represent and warrant that You are legally entitled to grant the above license. You further represent and warrant that each employee of the Entity that submits Contributions is authorized to submit such Contributions on behalf of the Entity.

Except as warranted above, You provide Your Contributions on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON- INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE.

4. Covenants

You agree to promptly notify Berkeley Lab of any facts or circumstances of which you become aware that would make any representations herein inaccurate in any respect.

5. Miscellaneous

This Agreement shall be governed by and construed in accordance with the laws of the State of California, without regard to the conflict of laws provisions thereof.
Any provision of this Agreement that is determined to be unenforceable or unlawful shall not affect the remainder of the Agreement and shall be severable therefrom, and the unenforceable or unlawful provision shall be limited or eliminated to the minimum extent necessary to that this Agreement shall otherwise remain in full force and effect and enforceable.

This Agreement constitutes the entire agreement between the parties and supersedes any and all prior agreements between them, whether written or oral, with respect to the subject matter hereof.

This Agreement may be terminated by either party at any time for any reason, upon thirty (30) days prior written notice. Excepting Section 2 of this Agreement all other terms and conditions shall survive any such termination.

This Agreement may not be amended, modified or provision hereof waived, except in a writing signed by the parties hereto.
No waiver by either party, whether express or implied, of any provision of this Agreement, or of any breach thereof, shall constitute a continuing waiver of such provision or a breach or waiver of any other provision of this Agreement.

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