Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond.

Autor: Rambla J; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), PRBB, Barcelona, Spain., Baudis M; Department of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland., Ariosa R; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Beck T; Department of Genetics & Genome Biology, University of Leicester, Leicester, UK., Fromont LA; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Navarro A; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Department of Experimental and Health Sciences, IBE, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra. PRBB, Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Universitat Pompeu Fabra, Barcelona, Spain.; Barcelona Beta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain., Paloots R; Department of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland., Rueda M; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Saunders G; European Infrastructure for Translational Medicine, EATRIS, Amsterdam, The Netherlands., Singh B; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Spalding JD; ELIXIR Finland; CSC - IT Center for Science Ltd, Espoo, Finland., Törnroos J; ELIXIR Finland; CSC - IT Center for Science Ltd, Espoo, Finland., Vasallo C; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Veal CD; Department of Genetics & Genome Biology, University of Leicester, Leicester, UK., Brookes AJ; Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
Jazyk: angličtina
Zdroj: Human mutation [Hum Mutat] 2022 Jun; Vol. 43 (6), pp. 791-799. Date of Electronic Publication: 2022 Apr 08.
DOI: 10.1002/humu.24369
Abstrakt: Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects.
(© 2022 The Authors. Human Mutation published by Wiley Periodicals LLC.)
Databáze: MEDLINE
Externí odkaz: