JGI Data Release Policy
The JGI Standard Data Release Policy for all projects is immediate public release, with the exception of the Bioenergy Research Centers (BRC). The data released includes the following:
- Sanger trace files are available from NCBI’s Trace Archive. Short reads (454 and Illumina) are deposited to NCBI’s Sequence Read Archive (SRA) as the data becomes available.
- Draft assemblies and preliminary automated annotation will be posted on the public JGI website and submitted publicly to GenBank as the data becomes available. The release of draft assemblies and preliminary automated annotation may not be simultaneous.
- Improved assemblies and annotation or other value-added data will be publicly released
as they become available.
- All data are subject to the data usage policies described at http://genome.jgi.doe.gov/pages/data-usage-policy.jsf.
- After the initial release to the PI, all assemblies and annotations (including finished or other value-added data) will be publically released immediately.
For BRC projects, the public release of Data can be delayed for up to six months after initial release to the PI.
This JGI Standard Data Release policy is effective for all CSP proposals/projects approved May 15, 2009 and later.
JGI Publication Policy
The JGI has a strong interest in seeing that the data produced by the facility result in scientific publications. The collaborator has 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 and any other contributions, such as assembly, finishing, analysis, annotation, verification, creation of genome browsers, etc.
The collaborators and JGI together reserve the right to publish the first analysis of genomic 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 with regard to genome analysis, annotation, and comparative analysis. If JGI personnel contribute substantially to post-sequencing work and the production of a manuscript, JGI contributors are expected to be credited as authors contributing to those aspects of the publication. If, by agreement with the collaborator, JGI staff take a lead role in the analysis, planning, writing, and editing of the manuscript, those individuals are expected to appear as first and/or senior authors of the paper.
Any external publication using data from the “Facilities Integrating Collaborations for User Science” (FICUS) JGI-EMSL initiative 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) initiative and used resources at the DOE Joint Genome Institute and the Environmental Molecular Sciences Laboratory, which are DOE Office of Science User Facilities. Both facilities are sponsored by the Office of Biological and Environmental Research and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).”
All other external publications using JGI data should contain the following Auspice Statement in the acknowledgments:
“The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.”
Peer Reviewed Articles and Technical Papers
DOE Funding Acknowledgment: please follow the DOE Office of Science guidelines for peer reviewed articles and technical papers: http://science.energy.gov/funding-opportunities/acknowledgements/
JGI Drafting Policy
Prokaryote Isolate Projects
At the time of approval, prokaryotic isolate projects at the JGI are expected to produce either a Minimal Draft genome or an Improved Draft genome.
JGI Prokaryote Minimal Draft Standards
- Illumina Std library coverage at 200x coverage
JGI Prokaryote Improved Draft Standards
- PacBio 10kb library at 120x coverage
- Library sequence quality control
- Contamination removal
- Artifact removal
- Identity verification
- Automated HGAP assembly
At the time of approval, eukaryotic projects at the JGI are expected to produce a draft genome. Projects are prioritized for further genome improvement based upon DOE mission relevance and feasibility.