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

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dc.contributor.author Rambla de Argila, Jordi
dc.contributor.author Baudis, Michael
dc.contributor.author Ariosa, Roberto
dc.contributor.author Beck, Timothy
dc.contributor.author Fromont, Lauren A.
dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-
dc.contributor.author Paloots, Rahel
dc.contributor.author Rueda, Manuel
dc.contributor.author Saunders, Gary
dc.contributor.author Singh, Babita, 1986-
dc.contributor.author Spalding, J. Dylan
dc.contributor.author Törnoos, Juha
dc.contributor.author Vasallo, Claudia
dc.contributor.author Veal, Colin D.
dc.contributor.author Brookes, Anthony J.
dc.date.accessioned 2022-05-30T10:28:25Z
dc.date.available 2022-05-30T10:28:25Z
dc.date.issued 2022
dc.identifier.citation Rambla J, Baudis M, Ariosa R, Beck T, Fromont LA, Navarro A et al. Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond. Hum Mutat. 2022 Jun;43(6):791-799. DOI:10.1002/humu.24369
dc.identifier.issn 1059-7794
dc.identifier.uri http://hdl.handle.net/10230/53310
dc.description.abstract 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.
dc.description.sponsorship This study was funded by ELIXIR, the research infrastructure for lifescience data and also by La Caixa Foundation (grant number 004745/ 008034). Tim Beck was supported by a UKRI Innovation Fellowship at Health Data Research UK (MR/S003703/1). Anthony J. Brookes and Jordi Rambla were supported, in part, by the European Union's Horizon 2020 research and innovation program under the EJP RD COFUND‐EJP #825575. Michael Baudis acknowledges funding under the BioMedIT Network project of Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN)
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Wiley
dc.rights © 2022 Jordi Rambla et al. Human Mutation published by Wiley Periodicals LLC. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject.other Medicina
dc.subject.other Genòmica
dc.subject.other Programari
dc.title Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1002/humu.24369
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/825575
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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