title: Cafe Variome: general-purpose software for making genotype-phenotype data discoverable in restricted or open access contexts.
abstract: 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.
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Owen
authors.initials: O
authors.lastname: Lancaster
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Tim
authors.initials: T
authors.lastname: Beck
authors.affiliation: PhenoSystems SA, Belgium.
authors.forename: David
authors.initials: D
authors.lastname: Atlan
authors.affiliation: University Medical Center Groningen, The Netherlands.
authors.forename: Morris
authors.initials: M
authors.lastname: Swertz
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Dhiwagaran
authors.initials: D
authors.lastname: Thangavelu
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Colin
authors.initials: C
authors.lastname: Veal
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Raymond
authors.initials: R
authors.lastname: Dalgleish
authors.affiliation: Department of Genetics, University of Leicester, Leicester, UK.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Brookes
mesh_terms: D016206:Databases, Bibliographic; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D033181:Information Dissemination / Q000379:methods*; D010641:Phenotype; D035583:Rare Diseases / Q000235:genetics*; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser
keywords: Cafe Variome; Matchmaker Exchange; data discovery; genotype-phenotype; rare disease; software