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.

The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

“…Multiple projects have addressed this need by developing platforms that use genotype and phenotype‐driven matching algorithms to identify cases with common phenotypes and disrupted genes [Washington et al., ; Gonzalez et al., , Swaminathan et al., , Gonzalez et al., , Robinson et al., ; Zemojtel et al., ; Buske et al., a; Lancaster et al., ; Sobreira et al., ]. However, no organized system existed to facilitate the interaction between these multiple disconnected projects (Fig.…”

“…To enable these types of investigations, MME systems will need to designate datasets and provide services that allow searching without requiring data deposition of a patient case. Some MME services already have apportioned some or all of their data for open interrogation such as DECIPHER [Chatzimichali et al., ] and the Monarch Initiative [Mungall et al., ], or enable direct searches within private networks as in the case of Cafe Variome [Lancaster et al., ]. Others services are committed to supporting such activities in the future.…”

ABCMdb reloaded: updates on mutations in ATP binding cassette proteins

“…This warns about the possibility that the maintainer of a central database can decide any time to close a site temporarily or even permanently. This phenomenon could effectively be prevented by a federated approach such as Cafe Variome (60), containing a central server for efficient querying and several independently accessible locus-specific data stores. This type of approaches can fulfill the roles expected from a central site, and also maintain the distribution of data with higher persistency and help in avoiding even temporary inaccessibility.…”

“…This type of approaches can fulfill the roles expected from a central site, and also maintain the distribution of data with higher persistency and help in avoiding even temporary inaccessibility. Importantly, for this setup, standards, such as in the case of Cafe Variome, should be defined accurately to allow the communication between the nodes for query, access control and data exchange management (60). In addition, the web application on each node could be tuned according to the field of the given gene, similarly to how our web application includes sequence alignments and structures of ABC proteins.…”

Cohort Harmonization and Integrative Analysis From a Biomedical Engineering Perspective

“…Café Variome [14] provides a data discovery platform in order to make content available to data scientists and researchers. Users search for data records of desired studies and the list of matching records is exported.…”