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Metadata Stewardship in Genetic Research: Enabling a Research Community Toward Best-practice

Dr Libby LigginsA Blog post by Libby Liggins (2019 WDS Data Stewardship Award Winner)

For over four decades, scientists have been collecting genetic DNA sequence data for thousands of the world’s species. In the biodiversity and eco-evolutionary sciences, these data are generated to describe new species, define their evolutionary relationships, determine the levels of dispersal among populations, and assess levels of genetic diversity across a species range. The rate at which we accrue these DNA sequences has increased over time as the use of genetic data has diversified, and the sequencing technologies used to decode the DNA sequences of organisms have become faster, cheaper, and much higher through-put. As this trend continues into the future, it is anticipated that we may soon have more DNA sequences in a digital form than we have existing in the natural world.

This massive and growing data resource could now be consolidated for multiple species and populations and reused to better understand the world’s biodiversity at the genetic level. Genes are recognized as a fundamental component of the biodiversity hierarchy, but have received less attention than species- and ecosystem-level measures of biodiversity. In part, this may be due to synthetic analyses of genetic data being challenging and sometimes impossible, as there has been no concerted effort towards the curation and stewardship of this valuable data resource. While funding agencies and publishers advocate deposition of DNA sequence data in open-access repositories (such as the National Center for Biotechnology Information; and the European Bioinformatics Institute), they do not require the deposition of standardized metadata such as the sampling location, date, and habitat of the sampling event (Pope et al. 2015). This ‘metadata gap’ means that information essential for multispecies analyses to better understand biodiversity and evolutionary patterns across our globe, has not been readily available.

The Genomic Observatories MetaDatabase (GEOME; Deck et al. 2017) has recently provided a solution to this metadata gap. GEOME links ecologically and evolutionarily relevant metadata with DNA sequences uploaded to open-access repositories. The metadatabase incorporates the latest international standards for biodiversity and genomic data, and helps researchers store and access genetic data relevant to studies concerning large scale biodiversity and conservation problems. In conjunction with the open-access DNA sequence repositories, GEOME ensures that researchers and projects generating genetic data can adhere to the FAIR Principles (Findable, Accessible, Interoperable, Reusable; Wilkinson et al. 2016), promoting research community best-practice.

IRA MOANA

The Ira Moana Project logo. The Māori phrase Ira Moana could be interpreted as meaning ‘ocean genes’ or ‘dot in the ocean’. Both seem appropriate when thinking about the scale of DNA in the vastness of the ocean. The use of te reo Māori (Māori language) resonates with the project objectives that are uniquely New Zealand, as is the Māori language. Yet, moana is used to describe the ocean by many Pacific nations, reminding us of the connections that New Zealand’s biodiversity has with the wider Pacific region.

The Ira Moana Project has partnered with GEOME both to enable a collaborative network of researchers to adhere to these standards in community best-practice, and deliver a searchable metadatabase for the genetic data of Aotearoa New Zealand’s marine organisms. The Project aims to build and maintain the most comprehensive national database of marine genetic data in the world, ensuring kaitiakitanga (guardianship and stewardship) and creating opportunities for data synthesis to inform New Zealand’s future research directions and conservation decisions. The Ira Moana Project builds on the success of the Diversity of the Indo-Pacific Network (DIPnet) that through the use of GEOME and multi-national collaboration, has created the largest population genetic database in the world. DIPnet consolidated over 200 genetic datasets for Indo-Pacific marine organisms, and is now delivering novel biodiversity insights for the Indo-Pacific Ocean (e.g., Crandall et al. 2018), which is the largest and one of the most threatened biogeographic regions on our globe.

The Ira Moana Project is similarly founded in concern for the marine environment. New Zealand is a marine nation—we have one of the largest exclusive maritime economic zones in the world, which sustains our marine and tourism industries, and provides significant recreational and social benefits for New Zealanders. Nationally, and as global citizens, we are under pressure to make informed decisions regarding commercial and recreational activities, and how they can be balanced with the protection of our marine ecosystems. Such decisions of environmental, economic, and societal impact need to be transparent and based on robust information, as well as including knowledge about biodiversity that stretches from ecosystems to genes. The Ira Moana Project has established that there are over 430 genetic datasets for New Zealand marine organisms, and is now working to consolidate these data for the benefit of future researchers and generations of New Zealanders.

GEOME

The data lifecycle in genetic research. DNA sequence data is routinely deposited into open-access genetic data repositories (under OUTPUTS). Despite metadata being accrued at every step of research (*), starting with COLLECTION, the practice of depositing metadata into repositories such as the Genomics Observatory Metadatabase (GEOME) is very recent. The Ira Moana Project is one of the project’s using the infrastructure provided by GEOME. Stewardship of metadata alongside DNA sequence data ensures that genetic research in the biodiversity, ecological, and evolutionary sciences can be reproducible, the genetic data can be re-used, and that the provenance of the genetic data and the rights of the local communities involved in the research are maintained.

As the first national project to make use of the GEOME infrastructure, the Ira Moana Project has worked with GEOME to extend the capability of the metadatabase to additionally acknowledge indigenous rights. It has become apparent that what is considered fair and equitable research practice within the research community, may not be fair and equitable within broader society. Through collaboration with Local Contexts and Te Mana Rauranga (the Māori Data Sovereignty Network), the Ira Moana Project and GEOME are now beta-testing the capacity for researchers to add Notices (such as the Traditional Knowledge Notice; TK Notice) and new Biocultural Labels as metadata for DNA sequence data. Notices signal that there are accompanying Indigenous rights needing further attention for any responsible and equitable future use of the data. Biocultural Labels further allow the addition of provenance information and community expectations for future use based on Indigenous Data Sovereignty principles—including the CARE Principles (Collective Benefit, Authority to Control, Responsibility, Ethics) launched by the Global Indigenous Data Alliance—thereby enabling Indigenous stewardship and persistent recognition of Indigenous rights within an international framework (complying with the Nagoya Protocol to the Convention on Biological Diversity). The implementation of Notices and Biocultural Labels using GEOME infrastructure is a first for a biological resource and for genetic data, establishing new ethical standards in this research community.

Workshops and datathons for New Zealand researchers have encouraged uptake and use of the metadata infrastructure provided through the Ira Moana Project and GEOME. There are now greater than 85 researchers who have joined the Ira Moana Project Network; being part of the network means being ‘on-board’ both with the things that the Ira Moana Project is trying to achieve for New Zealand, and the metadata standards that GEOME is accommodating for researchers worldwide. As there is a global community of researchers who generate genetic data, it will be some time before there is universal uptake of these newly recognized standards of best-practice. Nonetheless, we should be encouraged by the fact that as a community, we have made similar transformations in our practice in the past; since the introduction of the Joint Data Archiving Policy, it has been considered standard practice to deposit genetic data into open-access repositories. As such, we anticipate that the Ira Moana Project metadatabase will continue to grow and serve New Zealander’s, and there will be increasing uptake of the services that GEOME provides to the research and wider community.

Literature cited
 – Crandall ED, Riginos C, Bird CE, Liggins L, Treml E, Beger M, Barber PH, Connolly SR, Cowman PF, DiBattista JD, et al. 2019. The molecular biogeography of the Indo-Pacific: Testing hypotheses with multispecies genetic patterns. Global Ecology and Biogeography. 58(5):403–418.
 – Deck J, Gaither MR, Ewing R, Bird CE, Davies N, Meyer C, Riginos C, Toonen RJ, Crandall ED. 2017. The Genomic Observatories Metadatabase (GEOME): A new repository for field and sampling event metadata associated with genetic samples. PLoS Biology. 15(8):e2002925.
 – Pope LC, Liggins L, Keyse J, Carvalho SB, Riginos C. 2015. Not the time or the place: the missing spatio‐temporal link in publicly available genetic data. Molecular Ecology. 24(15):3802-9.
 – Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 3