Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond.
Beacon
GA4GH
REST API
clinical genomics
data discovery
data sharing
Journal
Human mutation
ISSN: 1098-1004
Titre abrégé: Hum Mutat
Pays: United States
ID NLM: 9215429
Informations de publication
Date de publication:
06 2022
06 2022
Historique:
revised:
07
03
2022
received:
29
09
2021
accepted:
12
03
2022
pubmed:
18
3
2022
medline:
25
5
2022
entrez:
17
3
2022
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 35297548
doi: 10.1002/humu.24369
pmc: PMC9322265
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
791-799Subventions
Organisme : Medical Research Council
ID : MC_PC_18031
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_19024
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S003703/1
Pays : United Kingdom
Informations de copyright
© 2022 The Authors. Human Mutation published by Wiley Periodicals LLC.
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