Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond.
Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond.
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DOI：
10.1002/humu.24369
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发表时间：
2022-06
期刊：
影响因子：
3.9
通讯作者：
Brookes, Anthony J.
中科院分区：
文献类型：
--
作者：
Rambla, Jordi;Baudis, Michael;Ariosa, Roberto;Beck, Tim;Fromont, Lauren A.;Navarro, Arcadi;Paloots, Rahel;Rueda, Manuel;Saunders, Gary;Singh, Babita;Spalding, John D.;Tornroos, Juha;Vasallo, Claudia;Veal, Colin D.;Brookes, Anthony J.
Beacon是由全球基因组学与健康联盟（GA 4GH）发布的基本数据发现协议。Beacon协议第1版的主要目标是测试广泛共享人类基因组数据的可行性，方法是对Beacon提供商托管的数据集中是否存在给定变体的查询提供简单的“是”或“否”回答。这一概念的普及促进了第2版的设计，该版本更好地服务于真实的世界需求，并解决了临床基因组学研究和医疗保健的需求，正如几个贡献项目和组织所评估的那样。特别是，罕见疾病遗传学和癌症研究将受益于新的病例水平和基因组变异水平的请求，以及更丰富的表型和临床查询的实现以及对模糊搜索的支持。Beacon被设计为一种“通用弗兰卡”，用于连接托管在具有不同和丰富界面的软件解决方案中的数据集合。Beacon版本2与流行的标准（如Phenopackets，OMOP或FHIR）一起工作，允许实施联盟在信标响应中返回匹配，并提供到其首选数据交换格式的切换。其他研究领域正在探索该协议，并在几个国际项目中进行测试。Beacon是由全球基因组学与健康联盟（GA 4GH）发布的基本数据发现协议。Beacon版本2服务于真实的世界需求，并解决了临床基因组学研究和医疗保健的需求，允许实施联盟在信标响应中返回匹配，并提供到其首选数据交换格式的切换。Beacon被设计为一种“通用弗兰卡”，用于连接托管在具有不同和丰富界面的软件解决方案中的数据集合。信标查询可以直接或通过信标网络发送到信标实例。如果用户被正确授权，则响应可以是是/否、计数或细节。
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. Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). Beacon version 2 serves real world requirements and addresses the needs of clinical genomics research and healthcare, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. Beacon is designed as a “lingua franca” to bridge data collections hosted in software solutions with different and rich interfaces. Beacon queries could be send to Beacon instances directly or via Beacon networks. The response could be yes/no, counts or details if the user is properly authorized.
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影响因子：
14.9
作者：
Harrison PW;Ahamed A;Aslam R;Alako BTF;Burgin J;Buso N;Courtot M;Fan J;Gupta D;Haseeb M;Holt S;Ibrahim T;Ivanov E;Jayathilaka S;Balavenkataraman Kadhirvelu V;Kumar M;Lopez R;Kay S;Leinonen R;Liu X;O'Cathail C;Pakseresht A;Park Y;Pesant S;Rahman N;Rajan J;Sokolov A;Vijayaraja S;Waheed Z;Zyoud A;Burdett T;Cochrane G
通讯作者：
Cochrane G
影响因子：
14.9
作者：
Cezard T;Cunningham F;Hunt SE;Koylass B;Kumar N;Saunders G;Shen A;Silva AF;Tsukanov K;Venkataraman S;Flicek P;Parkinson H;Keane TM
通讯作者：
Keane TM
影响因子：
3.9
作者：
Lancaster, Owen;Beck, Tim;Brookes, Anthony J.
通讯作者：
Brookes, Anthony J.
影响因子：
4.5
作者：
Cline, Melissa S.;Liao, Rachel G.;Tavtigian, Sean
通讯作者：
Tavtigian, Sean
DOI：
10.1093/database/baab043
发表时间：
2021-07-17
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Huang Q;Carrio-Cordo P;Gao B;Paloots R;Baudis M
通讯作者：
Baudis M