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The Cafe Variome approach changes the nature of the problem, by converting it to the challenge of enabling fully open and comprehensive “data discovery” (i.e., making the existence rather than the substance of the data openly accessible), for example, between networks of diagnostic laboratories or disease consortia that know/trust each other and share an interest in certain causative genes or diseases. This provides a mechanism for the discovery of rare sequence variants or patients with rare disease phenotypes.
Cafe Variome is not a database, but instead aims to be a “shop window” for openly searching/discovering what data exist. The system allows users to openly search the full content of the data, in sophisticated ways, and thereby determine whether or not a record of interest exists in an information resource. Users of the system can subsequently access the hit data (according to pre-set permissions) in line with one of the following conditions:
Open Access: the user may access variant and patient records directly and freely
Linked Access: the user can view summary data and is provided with a link to the source database to access the full record
Restricted Access: the user may access variant and patient records if they belong to a pre-approved group or must request access from the data owner to the full record
Cafe Variome offers a complete data sharing software solution (either a hosted or an “in-a-box” solution) all controlled by an intuitive administrator dashboard, which gives owners complete control over their data and installation. Dashboard configuration options include a content management system for adding/editing custom pages and menus, full control over site appearance (logo, colours, backgrounds, themes). Easy import of source data via templates, control over how searches are performed and results are displayed (ordering and specifying of fields and which fields can be searched) and a comprehensive access-control system for users and groups.
A sophisticated “Google-like” query interface allows users to form complex queries to interrogate and discover data across an installation. Additionally, multiple installations can be connected together to form federated networks to allow controlled queries across nodes within the network.
Each variant in the system can be annotated with any number of terms from any of the NCBO BioPortal phenotype ontologies. This flexibility allows a variant to be associated with a single disease term, or a complex combination of phenotype descriptions. An admin tool generates an up-to-date searchable term tree for all ontologies used in the annotations. This functionality makes use of the BioPortal API to ensure the latest version of all ontologies, and associated terms, are available to the user.