JGI Data Release Policy
The JGI Standard Data Release Policy is immediate public release for all user projects accepted through the Community Science Program (CSP), Facilities Integrating Collaborations for User Science (FICUS) or Bioenergy Research Centers (BRCs). The data released includes the following:
- Raw sequence data: fastq or other file formats as appropriate are deposited to NCBI’s Sequence Read Archive (SRA) after completion of standard analysis as described in the product catalog.
- Genome projects: assemblies and annotations are posted to JGI portals as soon as each genome project is complete. Microbial sequences (raw data and assembled contigs) are released after assembly and annotation in IMG. Fungal and plant sequences are released after assembly and annotation with RNA-seq data.
- Functional genomics data (e.g. resequencing and transcriptomes): analysis files, including alignments to reference genomes, are released upon completion of standard deliverables as described in the product catalog.
- Improved assemblies and annotations and associated data will be publicly released as soon as complete.
This JGI Standard Data Release policy is effective for all user proposals/projects approved May 15, 2009 and later. All data are subject to the data usage policies described at http://genome.jgi.doe.gov/pages/data-usage-policy.jsf.
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).”
Any external publication using data from the “Facilities Integrating Collaborations for User Science” (FICUS) JGI-NERSC 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 (JGI) and the National Energy Research Scientific Computing Center (NERSC). Both are DOE Office of Science User Facilities sponsored by the Office of Biological and Environmental Research (JGI) and the Office of Advanced Scientific Computing Research (NERSC) and operated under Contract No. DE-AC02-05CH11231.”
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.”
Acknowledgment of Federal Support
DOE Funding Acknowledgment: please follow the DOE Office of Science guidelines for news releases: http://science.energy.gov/funding-opportunities/acknowledgements/