Federated discovery and sharing of genomic data using Beacons.
journal contribution
posted on 2019-05-22, 14:08 authored by Marc Fiume, Miroslav Cupak, Stephen Keenan, Jordi Rambla, Sabela de la Torre, Stephanie O. M. Dyke, Anthony J. Brookes, Knox Carey, David Lloyd, Peter Goodhand, Maximilian Haeussler, Michael Baudis, Heinz Stockinger, Lena Dolman, Ilkka Lappalainen, Juha Törnroos, Mikael Linden, J. Dylan S Spalding, Saif Ur-Rehman, Angela Page, Paul Flicek, Stephen Sherry, David Haussler, Susheel Varma, Gary Saunders, Serena ScollenThe Beacon Project (beacon-project.io) is a GA4GH initiative that is
developing an open specification for genetic variation discovery and
sharing. The project is demonstrating the willingness of international
organizations to work together to define standards for, and actively engage
in, genomic data sharing. In the two years since the project’s inception, over
90 Beacons have been lit by 35 organizations serving over 200 datasets.
These datasets are searchable individually or in aggregate via the Beacon
Network (beacon-network.org), a federated search engine across the
world’s public beacons. Beacons serve large, diverse, valuable collections
of genomics datasets, showing the viability of a global federated model for
genomics data discovery and sharing through a simple and securable
technical protocol. With continued adoption, Beacons will produce a large
network of searchable genomics datasets whose global representation and
accessibility will unlock potential for new genomics-derived discoveries
and applications in medicine.
Funding
J. Ostell conceived the project; Global Alliance for Genomics & Health provided substantial guidance and support. The Beacon Project team designed and developed the Beacon API. Members of various organizations implemented Beacons and contributed to its APIs. We are thankful for data contributors who elect to share their data. M.F. and S.O.M.D. are supported by Genome Quebec, Genome Canada, the Government of Canada, and the Ministère de l’Économie, Innovation et Exportation du Québec (Can-SHARE grant 141210); S.O.M.D. is supported by the Canadian Institutes of Health Research (grants EP1-120608; EP2-120609) and the Canada Research Chair in Law and Medicine; M.H. is supported by BD2K NIH/NCI 5U54HG007990-02; S. Scollen, S.V., M.B., I.L., J.T., S.U.-R., S.d.l.T., M.L., H.S. and the EGA are supported by ELIXIR, the research infrastructure for life-science data. This work was supported by ELIXIR-EXCELERATE, funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (J.D.S., I.L.), the Wellcome Trust grant numbers WT201535/Z/16/Z (P.F.) and WT098051 (S.K., D.L., P.F.), and the European Molecular Biology Laboratory (P.F., S.K., J.D.S., I.L.); A.J.B. is supported by the European Union FP7 Programme ‘EMIF’ IMI-JU grant no. 115372, and H2020 Programme ‘GCOF’ grant no. 643439.
History
Citation
Nature Biotechnology, 2019, 37 (3), pp. 220-224Author affiliation
/Organisation/COLLEGE OF LIFE SCIENCES/Biological Sciences/Genetics and Genome BiologyVersion
- VoR (Version of Record)
Published in
Nature BiotechnologyPublisher
Nature Research (part of Springer Nature)eissn
1546-1696Copyright date
2019Available date
2019-05-22Publisher DOI
Publisher version
https://www.nature.com/articles/s41587-019-0046-xNotes
Publisher Correction 20 March 2019 https://doi.org/10.1038/s41587-019-0094-2 : In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, Toronto, Ontario, Canada. The error has been corrected in the HTML and PDF versions of the article.Language
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