Resources
Documentation and Websites
Implementation Toolkits
- Beacon Specification
- Beacon Specification Documentation
- Beacon V2 PI GitHub
- Beacon V2 PI Documentation
- Progenetix Bycon GitHub
- Progenetix Bycon Documentation
- Cafe Variome site
- Beacon Network GitHub
- Beacon Template UI
- sBeacon
- AskBeacon
Helpful Resources
- Beacon as GA4GH Standard
- CRG Beacon Verifier - configuration validation of Beacon instances
- BSC Validator - configuration validation of Beacon instances
- Pheno-Ranker - two-sided comparison of Phenopackets v2 and Beacon Friendly Format (BFF)
- ConvertPheno - two-sided conversion between various data standards and Beacon Friendly Format (BFF)
- CRG Phenopackets-to-BFF converter
Key publications
Twelve quick tips for deploying a Beacon¶
Lauren A. Fromont, Mauricio Moldes, Michael Baudis, Anthony J. Brookes, Arcadi Navarro, Jordi Rambla
PLoS Comput Biol. 2024 Mar 1; 20(3):e1011817. doi:10.1371/journal.pcbi.1011817. PMID: 38427629, PMCID: PMC10906850
In the age of data-driven biomedical research and clinical practice, the sharing of genomic and clinical data for health research and personalized medicine has become an important contributor to improved diagnosis and treatment. From the data owner’s perspective, potential benefits include improved treatments, personalization of healthcare practice, and more effective control of disease proliferation.
Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond¶
Jordi Rambla, Michael Baudis, Roberto Ariosa, Tim Beck, Lauren A. Fromont, Arcadi Navarro, Rahel Paloots, Manuel Rueda, Gary Saunders, Babita Singh, John D. Spalding, Juha Törnroos, Claudia Vasallo, Colin D. Veal, Anthony J. Brookes
Hum Mutat. 2022 Jun; 43(6):791-799. doi: 10.1002/humu.24369. PMID: 35297548, PMCID: PMC9322265
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.
Federated discovery and sharing of genomic data using Beacons¶
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 Spalding, Saif Ur-Rehman, Angela Page, Paul Flicek, Stephen Sherry, David Haussler, Susheel Varma, Gary Saunders & Serena Scollen
Nat Biotechnol. 2019 Mar; 37(3):220-224. doi: 10.1038/s41587-019-0046-x. PMID: 30833764, PMCID: PMC6728157
The Beacon Project is a Global Alliance for Genomics & Health (GA4GH) initiative that enables genomic and clinical data sharing across federated networks. The project is working toward developing regulatory, ethics and security guidance to ensure proportionate safeguards for the distribution of data according to the GA4GH-developed “Framework for Responsible Sharing of Genomic and Health-Related Data”.