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Cafe Variome: General‐Purpose Software for Making Genotype–Phenotype Data Discoverable in Restricted or Open Access Contexts
Author(s) -
Lancaster Owen,
Beck Tim,
Atlan David,
Swertz Morris,
Thangavelu Dhiwagaran,
Veal Colin,
Dalgleish Raymond,
Brookes Anthony J
Publication year - 2015
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.22841
Subject(s) - computer science , data sharing , world wide web , data discovery , interface (matter) , simple (philosophy) , software , data type , information retrieval , metadata , medicine , philosophy , alternative medicine , bubble , pathology , epistemology , maximum bubble pressure method , parallel computing , programming language
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), "linkedAccess" (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.