JGI Data Policy

Data produced and released by the US Department of Energy (DOE) Joint Genome Institute (JGI) are subject to the following Data Policy. It is our mission to support open data and information sharing. We also recognize the need to have a limited and time-sensitive protection of certain types of data to support their use by those generating data.

The JGI Data Policy applies to research data and analysis products (referred to as “data” for the remainder of this policy) produced through all user projects accepted FY22 and later through the Community Science Program (CSP), Facilities Integrating Collaborations for User Science (FICUS) initiative, Director’s Science (DS), Biological and Environmental Research Support Science (BERSS), or Bioenergy Research Centers (BRCs).

For sequencing or metabolomics projects: data are subject to a one-year embargo. For each data or analysis product (raw or processed), the embargo starts at completion of standard deliverables as described in the product catalog. At the end of the embargo period data will be made publicly available on relevant JGI portals (i.e. JGI Genome/Data Portal, MycoCosm, PhycoCosom, Phytozome, or IMG) and outside repositories (e.g. NCBI SRA or GenBank) as described in the product catalog and are unrestricted for use.

For DNA synthesis projects: data are subject to a two-year embargo starting at construct or strain delivery. Detailed sequence information for constructs are made publicly available through the Inventory of Composable Elements (ICE) repository at the end of the embargo period.

During the embargo, proposal PIs, Co-PIs, and collaborators of any given proposal have full access to their data and may request full release to the public, ending the embargo at any point after data generation. The data will not be publicly available in JGI portals or outside repositories until the earliest of three points: (1) publication of the data (including, but not limited to, publication or citation of accession numbers in a peer-reviewed journal, or any public deposition of the data at outside repositories), (2) PI request to list data publicly, or (3) at the end of the embargo period. If data or analyses of the data are made publicly available in any format by the PI or collaborator during the embargo period, JGI will consider the embargo nullified. After the embargo period, JGI places no further restrictions on data availability or utilization except as outlined in the Publication Policy.

For questions about JGI policies, please contact Policy & Agreements Officer Grace Sprehn.

For a complete list of standard deliverables see the product catalog. All data are also subject to the Publication Policy below.

Legacy Data, Restricted Use, and Data Policy Transitions:

Previous JGI Data Release & Utilization Policies may be read in full here. The following is a summary and explanation of policies in place during the transition to the above JGI Data Policy.

Pre-FY22 proposals: Proposals accepted before FY22 are transitioning away from producing use-restricted data. JGI proposals typically include multiple projects of different types which can span several years. Projects are defined at proposal acceptance and may also be added during the proposal lifecycle based on scientific need. Proposals are considered complete when all agreed-upon projects are complete. This policy is applied at the project level to expedite the change in data policy. Data from projects for which JGI has not yet received samples as of Sep 30, 2021 are subject to a 2-year embargo to maintain the timeline for unrestricted data availability agreed to at proposal initiation. Data from projects that received samples before Sep 30, 2021 and are ongoing are subject to the 2-year use-restriction policy as described here. No single project has data under both use-restriction and embargo policies.

Use-restricted data: In past data policies, data were publicly visible in JGI systems only but use-restricted until publication by PIs or at a set time (most recently, two years after release to JGI portals). JGI will no longer produce use-restricted data except in already active projects as described above, but JGI portals will still host use-restricted data until the period of use-restriction expires. All use-restricted data have an associated date of use-restriction expiration. Use-restrictions are also lifted at publication of the data. In short, those users not involved with the proposal under which the data were generated who wish to include use-restricted data in publications, or who wish to redistribute data in any way are required to contact the proposal PI and receive permission for their planned work. It is the responsibility of the user to ensure they have taken all appropriate steps before publishing or otherwise making publicly available use-restricted data.

JGI Publication Policy

The JGI has a strong interest in seeing that the data produced by the facility result in scientific publications. JGI users and collaborators have the right to produce manuscripts for publication and the responsibility for leading the efforts to do so, and JGI expects acknowledgment (see Auspice Statement below) for the generation of sequence or metabolomic data, DNA synthesized, and any other contributions, such as assembly, analysis, annotation, verification, creation of genome browsers, etc.

The users, collaborators and JGI together aim to publish the first analysis of data produced at the facility, provided this is done in a timely fashion. The publications resulting from such efforts should specify the collaborative nature of the project, and authorship is expected to include all those contributing significantly to the work.

The JGI has significant experience and capabilities in the analysis, annotation, comparative analysis, and interpretation of sequence, metabolomics, and functional genomics data types as well as in advanced assembly and engineering strategies for DNA synthesis applications. If JGI personnel contribute substantially to data generation and analysis or DNA synthesis and engineering work in a way that goes beyond the deliverables for JGI standard products and/or make substantial intellectual contributions to the production of a manuscript, it is best practice to credit those individuals as authors on the publication for their contributions. Authorship arrangements should reflect the respective contributions of collaborators and users. For example if, by agreement with the collaborator, JGI staff take a lead role in the analysis, planning, writing, and editing of the manuscript, it is best practice for those individuals to appear as first and/or senior authors of the paper.

Auspice Statements

Including appropriate tracking numbers is critical to facilitating the tracking of publications and allowing connections between all systems to maximize the impact of user research. The crucial elements are proposal Award DOI(s), JGI’s ROR ID number, and DOE contract numbers.

Please include the appropriate Auspice Statement in any external publications, and include proposal Award DOIs following these guidelines:

If you use data from 3 or fewer JGI proposals, include those DOIs in the auspice statement where indicated.
If you use data from 4 or more proposals, include those DOIs in a data availability section.
If it is impossible (for word limits or other reasons) to include all of the DOIs for proposals you accessed in the data availability section, include those DOIs in the supplemental materials for your publication.

Any external publication using data from the “Facilities Integrating Collaborations for User Science” (FICUS) JGI-EMSL program should contain the following Auspice Statement in the acknowledgments:

“(A portion of) This research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal: INSERT PROPOSAL AWARD DOI(S) HERE) and used resources at the DOE Joint Genome Institute (https://ror.org/04xm1d337) and the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).”

Any external publication using data from the “Facilities Integrating Collaborations for User Science” (FICUS) JGI-NERSC program should contain the following Auspice Statement in the acknowledgments:

“(A portion of) This research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal: INSERT PROPOSAL AWARD DOI(S) HERE) and used resources at the DOE Joint Genome Institute (JGI) (https://ror.org/04xm1d337) and the National Energy Research Scientific Computing Center (NERSC) (https://ror.org/05v3mvq14), which are DOE Office of Science User Facilities operated under Contract No. DE-AC02-05CH11231.”

All other external publications using JGI data produced under a specific proposal(s) and authored by that proposals PIs, Co-PIs, and collaborator(s), or any JGI-led publication without user data should contain the following Auspice Statement in the acknowledgments:

“The work (proposal: INSERT PROPOSAL AWARD DOI(S) HERE) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.”

Any external publication using JGI data that is not associated with a specific JGI proposal, and/or by authors other than PIs, Co-PIs, and collaborators of a JGI proposal should contain the following Auspice Statement in the acknowledgments:

“(A portion of) These data were produced by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337; operated under Contract No. DE-AC02-05CH11231) in collaboration with the user community.”

Acknowledgment of Federal Support

DOE Funding Acknowledgment: please follow the DOE Office of Science guidelines for news releases: https://science.osti.gov/Funding-Opportunities/Acknowledgements