Data Sharing and Management Best Practices
version 1.0-May 2022
Authors: Ann McCartney, Mark Blaxter, Robert Cook-Deegan, Richard Durbin , Linda Frisse, Janis Geary, Jessica Glass, Mitchell Head, Maui Hudson, Harris Lewin, James McInerney, Sadye Paez, Beckett Sterner, Krystal Tsosie, Marcela Uliano-Silva, Linda Wong.
A.Preamble:
The Earth BioGenome Project (EBP) is committed to the establishment of just, inclusive, equitable, and community-driven standards to streamline and scale-up the creation of a shared resource of reference genomic data for all of Earth’s eukaryotic biodiversity. As an international network of affiliated project networks, EBP recognizes the breadth and diversity of member institutions and their participants. To support EBP-affiliated projects in achieving our shared mission, EBP has appointed committees that focus on developing both technical as well as ethical, legal, and social standards that include justice, equity, diversity, and inclusion. Emphasizing that a robust ecosystem of data sharing and management is necessary to foster collaboration among EBP-affiliated projects and to maximize the scientific advances made possible by their work, these committees work to ensure that EBP affiliated projects, follow and uphold the highest standards in the production of reference genomes, including biodiversity data sharing and management.
EBP affirms that the protection and conservation of biodiversity is of common interest to all humanity. As such, EBP supports the establishment of responsible procedures for the sharing and management of biodiversity genomic data that maximize openness while respecting international and national legislation and the rights of Indigenous Peoples and Local Communities (IPLCs). EBP fully supports the ambitions of access and benefit-sharing (ABS) set forth in the Convention on Biological Diversity (CBD) and the Nagoya Protocol and is fully aligned with an open access policy for all digital sequence information (DSI). As biodiversity genomics data is fundamental to the advancement of science, society, and the well-being of humankind, EBP is committed to open access and sharing of this data to enable all nations and Peoples to progress and share the benefits of our global biodiversity. In pursuit of our mission to create a resource for global public good, EBP advocates and promotes all principles that assist in formulating a fair, universal, and practical protocol for ABS of DSI. Such principles will improve the ethical treatment of DSI for IPLCs, nations, and all societies of the world, while also advancing scientific goals.
In the midst of the planet’s sixth mass extinction, EBP strives to promote a collective, inclusive, equitable, and global response to this ongoing biodiversity crisis. Here, EBP outlines recommended best practices to be followed by affiliated projects for the sharing, management, and publication of genomic data. We include specific considerations for the management of data generated in partnerships formed between IPLCs and EBP-affiliated projects.
B. Best Practices:
For ethically and legally collected samples, EBP values all sequencing data generated and shared by affiliated projects and recognizes each dataset's contributions toward the goal of establishing reference sequences for all life on Earth. To completely catalog the genomic content of Earth’s biodiversity, EBP supports the generation of representative reference genomes for all species to a common set of standards of assembly quality (Lawniczak et al. 2022).
To be counted in the roster as an EBP representative reference genome, the genome assembly, underpinning raw data, and sample/specimen metadata should be shared in alignment with the FAIR (Wilkinson et al. 2016) and CARE (Carroll et al. 2020) principles. EBP fully supports an open access policy for DSI and expects all data to be contributed to the International Nucleotide Sequence Database Consortium (INSDC) through one of its founder nodes: European Nucleotide Archive, GenBank, and DNA Database of Japan, or via affiliated nodes.
EBP respects national sovereignty of biodiversity, the rights of IPLCs, and that open sharing through INSDC for some affiliated projects may be prohibited or delayed due to national law and regulations, legal agreements, or local organizational practices. In such cases, data should be shared using the FAIR and CARE principles and stored in an internationally recognized and stably funded data repository that follows the TRUST principles (Lin et al. 2020), working toward open release in INSDC.
EBP is acutely aware that the resources required for reaching its high data quality as well as management and sharing standards are not equally distributed globally, or even within nation states, and that there is a risk of asymmetrical and inequitable flow of sequence data. Highly resourced EBP-affiliated projects should not disproportionately benefit from the sequencing of biodiversity situated in lower- and middle-income nation states. In such cases, EBP strongly encourages highly resourced projects to support lower-resourced projects, to the best of their ability, to reduce barriers to producing and analyzing EBP representative reference genomes that meet the standards of assembly quality. Such a procedure will also enable the release of these data in compliance with the FAIR, CARE and TRUST principles in a timely fashion. Assistance may include, but is not limited to funding, collaboration, technology transfer, training, and general capacity building.
C. Considerations for sharing and managing data when partnering with Indigenous Peoples and Local Communities:
The term Indigenous Peoples and Local Communities has been utilized internationally in recognition of the Peoples and Communities who have a long association with the lands and waters that they have traditionally lived on or used. EBP acknowledges the failures in biodiversity research that have caused exploitation, unfair distribution of benefits, stigmatization, marginalization, and disenfranchisement of IPLCs across the globe (Agrawal 2002; Hudson et al. 2020; Collier-Robinson et al. 2019). The inclusion and recognition of the rights and needs of IPLCs is essential to realize the mission of EBP. EBP recognizes the United Nations Declaration of the Rights of Indigenous Peoples (UNDRIP) (Assembly 2007), the Indigenous and Tribal Peoples Convention, 1989 (No. 169) (Indigenous and Tribal Peoples Convent...), CBD Article 8j, and the Nagoya Protocol (United Nations Environmental Programm...). EBP affirms its commitment to supporting trustworthy and responsible genomics research practices that prioritize cultivating sustained relationships, support access and benefit-sharing with IPLC partners, and promote both the CARE and FAIR principles.
To be accepted as contributing to the goals of EBP, biological samples or Traditional Knowledge obtained from IPLCs’ lands and Peoples must be ethically and legally obtained. EBP affirms the importance of an engagement with potential IPLC partners in which the data-sharing goals and mission of the EBP accommodate the priorities, needs and preferences of the IPLCs in a clear and transparent manner. As with all EBP reference genomes, reference genomes generated in partnership with IPLCs should be accompanied by both FAIR and CARE aligned metadata. EBP emphasizes the specific importance of including accurate origin and provenance information for both samples and data and ensuring all metadata fields are shared and respectful of any cultural sensitivities. When partnering with IPLCs, EBP promotes data sharing practices that enable appropriate attribution, appropriate access, and appropriate authority.
D. Publication Best Practices:
The EBP community is built upon collaboration, cooperation, fair attribution, and trust. EBP commends affiliated projects that promote the open and responsible sharing and reuse of data prior to first publication and supports rapid formal publication of EBP reference genomes where credit is fairly attributed to all contributors. However, EBP respects that some affiliates may wish to safeguard the interests of their members to the rights to first publication through a publication embargo period codified in an explicit Publication Policy. As a member of the EBP community, each EBP-affiliated project is expected to respect the standing Publication Policies of all members. For EBP-affiliated projects with IPLC partners, all mutually agreed upon research dissemination and publication strategies should also be respected.
E. References
Carroll, Stephanie Russo, Ibrahim Garba, Oscar L. Figueroa-Rodríguez, Jarita Holbrook, Raymond Lovett, Simeon Materechera, Mark Parsons, et al. 2020. “The CARE Principles for Indigenous Data Governance.” Data Science Journal 19 (November). https://doi.org/10.5334/dsj-2020-043.
Collier-Robinson, Levi, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand, Aisling Rayne, Makarini Rupene, Channell Thoms, and Tammy Steeves. 2019. “Embedding Indigenous Principles in Genomic Research of Culturally Significant Species: A Conservation Genomics Case Study.” New Zealand Journal of Ecology 43 (3). https://doi.org/10.20417/nzjecol.43.36.
Indigenous and Tribal Peoples Convention, 1989 (No. 169). 2002.
Lawniczak, Mara K. N., Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, et al. 2022. “Standards Recommendations for the Earth BioGenome Project.” Proceedings of the National Academy of Sciences of the United States of America 119 (4). https://doi.org/10.1073/pnas.2115639118.
Vogel, Gretchen. 2019. “Natural History Museums Face Their Own Past.” Science 363 (6434): 1371–72.