Introductory Comments

U.S. Department of Energy (DOE) Joint Genome Institute (JGI) Data Release and Utilization Policies aim to balance the DOE mandate to have data broadly accessible to the scientific community while retaining the ability of the JGI user PIs to publish the primary report of their data without concern of preemption by others. We are aware of the need to reconcile this apparent conflict. Our aim is to continue to foster and enable open science while protecting and supporting users by ensuring they receive credit for the substantial efforts and resources that lead to data generation.

We would like to solicit community feedback on proposed changes to our current policies to gain a better understanding of how this change may affect data-producing users and other users (i.e., users who download, analyze, and publish using data created from a proposal on which they were not involved), and how you, the research community, would like to see JGI provide leadership to the community for data utilization.

Current Policy 

This summary of current JGI Data Release and Utilization Policies does not serve as policy itself. Please find complete policies here.

Data produced for user projects accepted through CSP, FICUS, BRCs, BERSS or Director’s Science projects are released to the public pre-publication by JGI to JGI portals and appropriate community databases such as NCBI’s Sequence Read Archive (SRA), but are subject to a period of exclusive publication rights under JGI’s policy. There is no true embargo on data from these projects. Rather, use of the data for publication or redistribution is restricted by the JGI Data Utilization Policy, summarized below. 
  • The applicable utilization policy depends on the date a user proposal was accepted, reflecting a policy change which took place in November 2018
  • For proposals accepted before Nov 2018, usage restrictions lift upon publication of the primary analysis report of the dataset by the PIs
  • For proposals accepted post Nov 2018, usage restrictions lift upon either publication of the primary analysis report by the PIs OR 2 years after public release (whichever is earliest)

Quick guide: Is this data use-restricted?
  • During this period of restriction, potential other users must contact the main PI and obtain permission to:
    • Publish articles containing the data or analyses of the data
    • Repackage or redistribute raw sequence reads and/or assemblies 
  • Once the primary analysis report is published by PIs, all JGI usage restrictions are lifted and JGI no longer limits publication rights. Subsequent analyses may not be reserved once the primary report is published. Publication of a smaller portion of the dataset either by PIs or (after permission is granted) by other users does not lift usage restrictions as outlined above, and must include appropriate acknowledgment as described in the Utilization Policy.
  • DNA synthesis projects are subject to a separate release policy which requires sequence information for constructs be released publicly 2 years after delivery to users.
  • At all times, appropriate auspice statements, acknowledgements and citations (including of any assigned DOIs) must be included as listed on relevant portals and the policy page linked above.
Currently, data users agree to these policies when accessing any JGI portal or downloading data, but we are unable to place restriction information on NCBI entries per their own policies. Because raw and processed data is eligible to be released to NCBI immediately after analysis is completed, data in NCBI may still be in a restricted use period according to JGI policy, but we are unable to clearly mark the status of use restrictions on the NCBI entry itself. The proposed changes aim to address this issue.
Proposed changes

JGI has support from DOE to delay the release of sequencing data to NCBI until the utilization restrictions are lifted. If this proposed policy change is adopted, user data would still be made available under the current immediate release policy on JGI portals under the terms of the JGI’s Data Release and Utilization Policies. In JGI portals, these policies must be acknowledged before data can be accessed or downloaded, providing JGI with means for enforcement of use restrictions if needed.

DOE would also like to reevaluate the current time period for exclusive use. Under the new policies data would be made public via appropriate public databases such as NCBI at the earliest of three points: publication of primary analysis report by JGI user PIs, after the set period of exclusive use expires, or at the request of the PIs.

With these policy changes in mind, JGI is also initiating changes to increase clarity and ease of use, including tagging use-restricted data sets in JGI portals (beyond existing publication flags).

Question Title

* 1. What is your current relationship with JGI?