Prerelease data usage and collaboration policy
R2K encourages the use of the genomic data we generate ahead of public release, in a collaborative fashion. The policy for pre-release data use and instructions on how to become an R2K collaborator can be found here. We anticipate that this policy will evolve over time as we accumulate data and refine our project goals
Rodent2K project.
A project is R2K if it agrees to this policy, and ultimately aims to achieve the 3.4.2.Q40 (c.s.m.Q40: contiguous/scaffold/map-chromosome/Qscore) assembly metric. This is at least a contig N50 of 1Mbp; a scaffold N50 of 10Mbp; >90% contains mapped to chromosomes; a consensus accuracy of Q40 or better.
Furthermore, a project is R2K if it agrees to place all the data in the public domain post-first publication, and to all core participants identified as R2K members.
R2K projects and their species targets will be visible on the R2K website, with an indication of methodology, expected timeline, flagship paper plan and core participants
Access to R2K genomes will be possible for R2K members following the submission of an application to be assessed by the executive committee (See point 3 for procedure).
Early access to R2K genomes will only be granted upon agreement with the R2K embargo policy, which requires that no publications including the R2K genomic data can be made until 18 months from the data freeze, or publication of the flagship paper – whichever comes first
Core Participants
Core participants are defined as the funders/grant recipients who fund the sequencing efforts, individuals who contribute to the official assembly, annotation and analysis of the genome, sample providers who provide flash-frozen tissues for high-quality DNA extraction, and scientific proposers of a given project.
At the outset (where possible), core participants of any R2K project are identified and set. Core participants for each project will be listed on the members-only section of the R2K website. Core participants will be expected to be co-authors on the flagship publications for each subproject. Authorship of secondary publications will be negotiated on a case-by-case basis (see below).
Collaborations
To strengthen the impact and publications of a project, parties interested in collaborating on a scientific aspect of a project are welcome to apply to join a project as a collaborator:
Parties interested in collaborating on R2K projects should complete the online Collaboration Proposal form which can be found in the R2K member area. If you are not already a member of R2K, you can sign up.
Collaboration proposals will be considered on a rolling basis by the R2K executive committee. The decision to accept a collaboration proposal for a project is made by the executive and core participants of the project
A collaborator has access to all data as it is produced with the provision that they must guarantee to safeguard the data and that they do not release findings or data derived therefrom before the publication of the project’s primary paper.
A collaborator sees all project communications and is invited to all project meetings.
The work or findings of a collaborator may be included in a project’s primary paper at the decision of the core participants. Indeed this is the desired outcome. However, if a collaborator’s findings are not to be included, then they are free to produce an independent manuscript subject to coordinating submission with respect to a project’s primary/first paper. They may not publish any finding based on the data prior to the first flagship paper for the project. If collaborators make use of data relevant for multiple projects, this applies to the flagship papers for all relevant projects.
Policy Rodent 2K Ethical Sampling
In the spirit of collaboration in which the Rodent 2K project is founded, we expect all participants, collaborators, and supporters to engage in ethical sample collection, data sharing, and research practices. Although a comprehensive policy on ethical considerations is beyond the scope of Rodent 2K, we believe addressing such issues is warranted, particularly as they pertain to: (1) Sample Collection, (2) Sample Sharing, and (3) Sample Vouchers.
Sample Collection
It is critical that specimens and samples contributing to Rodent 2K are obtained legally and ethically. Legal requirements may vary by country and thus Rodent 2K participants are encouraged to work with in-country collaborators and partners to ensure local, national, and international aspects of specimen collection, export, and archiving are followed. Physical or digital records of all permits and official correspondence related to these activities should be maintained to address any questions related to their legal acquisition. Potentially relevant documents to include in such records include collecting permits, export permits, import permits, memorandums of understanding (MOUs), material transfer agreements (MTAs), mutually agreed terms (MATs), or prior informed consent (PIC) forms. Regulations of such activities invariably change through time, and thus it is important that whenever possible, all relevant documentation obtained at the time of collection are archived and linked to their associated specimens and samples. Ethical guidelines for collection of rodents also varies locally, regionally, nationally, and internationally and participants should ensure proper approval is provided by relevant authorities (e.g., International Animal Care and Use Committees) or that taxonomic-focused guidelines are adhered to (e.g., Sikes et al. 2016).
Sample Sharing
Sharing samples among collaborators, across institutions, and beyond borders is fundamental to achieving the goals of Rodent 2K. Guidelines for sample sharing already exist, and although not always perfect (see Alexander et al. 2021 or Colella et al. 2023), we refer all Rodent 2K participants to the following sources of information on best practices: The Nagoya Protocol (http://www.cbd.int/cop10/) and its associated Access Benefit Sharing principles (https://www.cbd.int/abs/), the FAIR guiding principles (Wilkinson et al. 2016), and the Earth BioGenome Project guidelines (Sherkow et al. 2022).
Sample Vouchers
The Rodent 2K project believes strongly in associating any tissue samples used for genome sequencing with a physical voucher specimen. Genomes with associated voucher specimens stored in publicly accessible collection facilities, such as natural history museums, ensure permanent verification of the samples identification, provide material for repeatable and extension of research questions, and creates a permanently archived specimen linked to standardized and publicly accessible metadata and permits (Bucnker et al. 2021; Thompson et al. 2021). In addition, promotion of permanent archiving of specimens and associated tissue samples can help promote in-country research and infrastructure in ways that samples in a private research lab freezer simply cannot (Colella et al. 2020). In addition, studies have shown that lethal sampling for deposition into natural history museums has minimal impact on rare and common species of rodents in the long-term (Hope et al. 2018). For species of conservation concern, we suggest following guidelines outlined in Clemann et al. (2018).
References
Alexander, G. J., Tolley, K. A., Maritz, B., McKechnie, A., Manger, P., Thomson, R. L. ., Schradin, C., Fuller, A., Meyer, L., Hetem, R. S. ., Cherry, M., Conradie, W., Bauer, A. M., Maphisa, D., O’Riain, J., Parker, D. M. ., Mlambo, M. C. ., Bronner, G., Madikiza, K., … Kerley, G. I. (2021). Excessive red tape is strangling biodiversity research in South Africa. South African Journal of Science, 117(9/10). https://doi.org/10.17159/sajs.2021/10787
Buckner JC, Sanders RC, Faircloth BC, Chakrabarty P. (2021). The critical importance of vouchers in genomics. eLife 10:e68264. https://doi.org/10.7554/eLife.68264
Clemann N, Rowe KM, Rowe KC, Raadik TA, Gomon MF, Menkhorst P, Sumner J, Bray D, Norman M, Melville J. (2014). Value and impacts of collecting vertebrate voucher specimens, with guidelines for ethical collection. Memoirs of Museum Victoria. 72: 141-53.
Colella JP et al. (2020) Build international biorepository capacity. Science 370,773-774. https://doi.org/10.1128/mbio.02698-20
Colella, J. P., Silvestri, L., Súzan, G., Weksler, M., Cook, J. A., & Lessa, E. P. (2023). Engaging with the Nagoya Protocol on Access and Benefit-Sharing: recommendations for noncommercial biodiversity researchers. Journal of Mammalogy, 104(3), 430-443. https://doi.org/10.1093/jmammal/gyac122
Hope, A. G., Sandercock, B. K., & Malaney, J. L. (2018). Collection of scientific specimens: Benefits for biodiversity sciences and limited impacts on communities of small mammals. Bioscience, 68(1), 35-42. https://doi.org/10.1093/biosci/bix141
Sherkow JS, Barker KB, Braverman I, Cook-Deegan R, Durbin R, Easter CL, et al. Ethical, legal, and social issues in the Earth BioGenome Project. Proc Natl Acad Sci U S A. 2022;119. doi:10.1073/pnas.2115859119
Sikes, R. S., & the Animal Care and Use Committee of the American Society of Mammalogists. (2016). Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education. Journal of Mammalogy, 97(3), 663-688. https://doi.org/10.1093/jmammal/gyw078
Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang MKhan FAA, Paul DLReeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. (2021). Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 12:10.1128/mbio.02698-20.
https://doi.org/10.1128/mbio.02698-20
Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A, et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3: 160018. doi:10.1038/sdata.2016.18
Additional Resources
Earth BioGenome Project- Sample Collecton and PRocessing Standards
https://www.earthbiogenome.org/sample-collection-processing-standards-2024
Africa BioGenome Project Sample Collection and Processing Sub-committee Terms of Reference
https://africanbiogenome.org/reports/sample-collection-and-processing/
Learn Nagoya
https://learnnagoya.com/