Cafe Variome: General-Purpose Software for Making Genotype-Phenotype Data Discoverable in Restricted or Open Access Contexts
Cafe Variome: General-Purpose Software for Making Genotype-Phenotype Data Discoverable in Restricted or Open Access Contexts
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DOI：
10.1002/humu.22841
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发表时间：
2015-10-01
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：
Lancaster, Owen;Beck, Tim;Brookes, Anthony J.
生物医学数据共享是可取的，但存在问题。数据“发现”方法建立数据的存在性而不是数据的实质精确地连接数据所有者和数据搜索者，从而促进数据共享。因此，Cafe Variome（http：www.cafevariome.org）旨在提供一种通用的、基于Web的数据发现工具，任何基因型-表型数据所有者或数据所有者网络都可以快速安装该工具，以使安全或敏感内容适当地可解密。可以容纳任何类型的数据字段或内容，从简单的ID和标签字段到基于本体的广泛的基因型和表型细节。该系统在数据前提供了一个“橱窗”，主要界面是一个简单的搜索框和一个功能强大的“查询生成器”，可以制定非常详细的查询。成功搜索后，报告的记录计数按“开放访问”（数据可直接访问）、“链接访问”（提供源链接）和“限制访问”（便利的数据请求和随后提供批准的记录）分组。管理员界面为系统配置提供了广泛的选项，可以建立高度定制的单站点或联合网络。目前的应用包括罕见疾病数据发现、患者匹配和Beacon Web服务。(C)2015 Wiley Periodicals，Inc.
Biomedical data sharing is desirable, but problematic. Data "discovery" approaches-which establish the existence rather than the substance of data-precisely connect data owners with data seekers, and thereby promote data sharing. Cafe Variome (http://www.cafevariome.org) was therefore designed to provide a general-purpose, Web-based, data discovery tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable. Data fields or content of any type can be accommodated, from simple ID and label fields through to extensive genotype and phenotype details based on ontologies. The system provides a "shop window" in front of data, with main interfaces being a simple search box and a powerful "query-builder" that enable very elaborate queries to be formulated. After a successful search, counts of records are reported grouped by "openAccess" (data may be directly accessed), "linked-Access" (a source link is provided), and "restrictedAccess" (facilitated data requests and subsequent provision of approved records). An administrator interface provides a wide range of options for system configuration, enabling highly customized single-site or federated networks to be established. Current uses include rare disease data discovery, patient matchmaking, and a Beacon Web service. (C) 2015 Wiley Periodicals, Inc.