Beacon

Enables researchers to discover new, relevant datasets while honouring patient consents and legal requirements

Overview

Summary Benefits Target users Announcements

One of the bottlenecks in human biomedical research is finding datasets that researchers can analyse using new approaches. Developed by the GA4GH Discovery Work Stream, the Beacon API is a simple data discovery tool that allows someone to search genomic and biomedical data worldwide, helping researchers find new datasets without compromising dataset privacy or ownership.

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Beacon helps researchers discover useful information about data they can study while helping data custodians securely share insights from their data with the world.

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Beacon

Benefits

Allows users to query for biological data, phenotypic/clinical data, and metadata
Accepts queries using semantic codes such as CURIEs (e.g. phenotypes, disease codes, sex, or age)
Shows who to contact or where the data could be accessed and which are the data use conditions in order to get the data
Offers the possibility to query for the annotations on the variants found, including expert or clinician conclusions — when available — on the pathogenicity of a specific mutation in an individual or its contribution to a particular phenotype
Gives information about cohorts and/or study

Target users

Researchers, clinicians, data generators, data custodians, data protection authorities, and developers

Announcements

Date	Title
30 January 2024	Join GA4GH Beacon Scouts

Title	Related Driver Projects and Organisations
ARGO Data Platform	ICGC ARGO
Australian Genomics Data Management Systems	Australian Genomics
BRCA Exchange	BRCA Challenge
CanDIG V2	Canadian Distributed Infrastructure for Genomics (CanDIG)
EJP-RD Beacon-in-a-Box	European Joint Programme on Rare Disease (EJP RD)
ELIXIR European Genome-phenome Archive (EGA)	European Genome-phenome Archive (EGA)
ELIXIR-Beacon	ELIXIR Beacon
Federated EGA	European Genome-phenome Archive (EGA), EMBL's European Bioinformatics Institute (EBI), Centre for Genomic Regulation
H3ABionet	Human Heredity and Health in Africa (H3Africa)
Variant Interpretation for Cancer Consortium (VICC) Meta-Knowledgebase (v1)	Variant Interpretation for Cancer Consortium (VICC)

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Publications Documents Videos

Publications

Title	Author(s)	Year
pgxRpi: an R/bioconductor package for user-friendly access to the Beacon v2 API	Zhao, H. et al. Zhao, H., Baudis, M.	2025
Use of Beacon v2 for Improving Genomics Based Research in a Clinical Setting	Naro, D. et al. Naro, D., Delgado, J., Llorente, S., Hernaez, M.	2024
Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond	Leist, I.C. et al. Leist, I.C., Rivas-Torrubia, M., Barturen, G., Gut, I.G., Rueda, M.	2024
Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data	Rueda, M. et al. Rueda, M., Ariosa, R., Moldes, M., Rambla, J.	2022
Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond	Rambla, J. et al. Rambla, J., Baudis, M., Ariosa, R., Beck, T., Fromont, L. A., Navarro, A., Paloots, R., Rueda, M., Saunders, G., Singh, B., Spalding, J. D., Törnroos, J., Vasallo, C., Veal, C. D., Brookes, A. J.	2022
International federation of genomic medicine databases using GA4GH standards	Thorogood, A. et al. Thorogood, A., Rehm, H.L., Goodhand, P., Page, A.J.H., Joly, Y., Baudis, M., Rambla, J., Navarro, A., Nyronen, T.H., Linden, M., Dove, E.S., Fiume, M., Brudno, M., Cline, M.S., Birney, E.	2021
Federated discovery and sharing of genomic data using Beacons	Fiume, M. et al. Fiume, M., Cupak, M., Keenan, S., Rambla, J., de la Torre, S., Dyke, S.O.M., Brookes, A.J., Carey, K., Lloyd, D., Goodhand, P., Haeussler, M., Baudis, M., Stockinger, H., Dolman, L., Lappalainen, I., Törnroos, J., Linden, M., Spalding, J.D., Ur-Rehman, S., Page, A., Flicek, P., Sherry, S.T., Haussler, D., Varma, S., Saunders, G., Scollen, S.	2019
Using High Performance Computing to Create and Freely Distribute the South Asian Genomic Database, Necessary for Precision Medicine in this Population	Shah, A.H. et al. Shah, A.H., Picker, J.D., Jamuar, S.S.	2017
Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services	Wan, Z. et al. Wan, Z., Vorobeychik, Y., Kantarcioglu, M., Malin, B.A.	2017
Aftermath of bustamante attack on genomic beacon service	Aziz, M.M. et al. Aziz, M.M., Ghasemi, R., Waliullah, M., Mohammed, N.	2017
Addressing Beacon re-identification attacks: Quantification and mitigation of privacy risks	Raisaro, J.L et al. Raisaro, J.L, Tramèr, F., Ji, Z., Bu, D., Zhao, Y., Carey, K., Lloyd, D., Sofia, H., Baker, D., Flicek, P., Shringarpure, S., Bustamante, C., Wang, S., Jiang, X., Ohno-Machado, L., Tang, H., Wang, X., Hubaux, J.P.	2017
Sharing Health-Related Data: A Privacy Test?	Dyke, S.O.M. et al. Dyke, S.O.M., Dove, E.S., Knoppers, B.M.	2016
RD-Connect: Data Sharing and Analysis for Rare Disease Research within the Integrated Platform and through GA4GH Beacon and Matchmaker Exchange	Roos, A. et al. Roos, A., Beltran, S., Piscia, D., Laurie, S., Protasio, J., Cañada, A., Fernández, J.	2016
Facilitating a Culture of Responsible and Effective Sharing of Cancer Genome Data	Siu, L.L. et al. Siu, L.L., Lawler, M., Haussler, D., Knoppers, B.M., Lewin, J.H., Vis, D.J., Liao, R.G.	2016

Documents

Date	Title
17 March 2025	GA4GH Implementation Forum (GIF) Ask Me Anything: Beacon
14 September 2023	Code of Ethics and Community Conduct (CECC)
10 May 2023	Meeting minutes: Discovery (2021 to 2023)
25 January 2019	Meeting minutes: Discovery (2019 to 2020)
22 January 2019	Meeting minutes: Discovery Beacon API (2022 to 2023)
25 September 2017	Meeting minutes: Discovery (2017 to 2018)

Videos

	Date	Title
	5 December 2019	Using the GA4GH toolkit: Beacon API V1.0.0 for genomic data discovery
	9 June 2015	GA4GH 3rd Plenary: Beacon project and data sharing APIs
	18 October 2014	GA4GH 2nd Plenary: Beacon project

Contributors Driver Projects

Contributors

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Michael BaudisBeacon LeadUniversity of Zurich, Zurich
Jordi RamblaBeacon LeadCentre for Genomic Regulation, Barcelona
Dixie BakerMartin, Blanck and Associates
Tim BeckUniversity of Nottingham
Sergi BeltranCNAG CRG, Barcelona, Spain
Guillaume BourqueMcGill University / Université McGill, Montréal, Canada
Michael BrudnoUniversity Health Network, Toronto, Canada
David BujoldMcGill University / Université McGill, Montréal, Canada
Salvador Capella-GutierrezBarcelona Supercomputing Center, Barcelona
Knox CareyIntertrust Technologies Corporation, Sunnyvale
Miro CupakVerily, South San Francisco, CA, USA
Joaquin DopazoProgress and Health Foundation
Marc FiumeDNAstack, Toronto
Paul FlicekUniversity of Cambridge, Cambridge
Lauren FromontCentre for Genomic Regulation, Barcelona
Gwênlyn GlusmanInstitute for Systems Biology, Seattle
Melissa HaendelUNC School of Medicine
Dean HartleyAutism Speaks, Princeton
Sumit JamuarGlobal Gene Corp, Hinxton
Saumya JamuarKK Women's and Children's Hospital
Patrick MageeDNAstack, Toronto
Alice MannWellcome Sanger Institute (WSI), Hinxton, UK
Mamana MbiyavangaUniversity of Cape Town, Cape Town
Arshiya Merchant
Jean MullerLaboratoire de génétique médicale (UMR_S 1112)
Heimo MuollerMedical Univerisity Graz
Rahel PalootsUniversity of Zurich, Zurich
Augusto RendonGenomics England
Manuel RuedaCentro Nacional de Análisis Genómico (CNAG), Barcelona
Babita SinghCentre for Genomic Regulation, Barcelona
Dylan SpaldingCSC – IT CENTER FOR SCIENCE
Morris SwertzUniversity Medical Center Groningen
Susheel VarmaInformation Commissioner's Office
Colin VealUniversity of Leicester, Leicester, UK
Brian WalshKnight Diagnostic Laboratories, Oregon Health & Science University, Portland
Christina YungOntario Institute for Cancer Research (OICR), Toronto, Canada, Indoc Research, Toronto
Joeri van der VeldeUniversity Medical Center Groningen

Driver Projects

Title	Thematic Area
Australian Genomics	Rare Disease Cancer Complex Traits
Canadian Distributed Infrastructure for Genomics (CanDIG)	Rare Disease Cancer Complex Traits Basic Biology
ELIXIR Beacon	Rare Disease Cancer Complex Traits Basic Biology
Human Heredity and Health in Africa (H3Africa)	Complex Traits Basic Biology
ICGC ARGO	Cancer
European Genome-phenome Archive (EGA)	Rare Disease Cancer Complex Traits Basic Biology
European Joint Programme on Rare Disease (EJP RD)	Rare Disease
Variant Interpretation for Cancer Consortium (VICC)	Cancer