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

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.This study was funded by ELIXIR, the research infrastructure for life-science data and also by LaCaixa 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).Peer reviewe