Cafe Rouge Wiki

This wiki aims to highlight the basic concepts of Cafe Rouge, logged in members of the group are able to edit these pages. Interested individuals are encouraged to join the group and actively participate with any discussions regarding the project.

Cafe Rouge Overview and Core Concept

Diagnostics laboratories assess DNA samples from many patients with various inherited disorders, and so produce a great wealth of data on the genetic basis of disease. Unfortunately, those data are not usually shared with others. To address this gross deficiency, we are constructing a system that will facilitate the automated transfer of diagnostic laboratory data to the wider community, via an Internet-based Café for Routine Genetic data Exchange (Café RouGE).

Diagnostic laboratories are not reluctant to release their data. Instead, the obstacles are merely practical: First, diagnostic laboratory personnel do not have time nor funding to manually submit data to Internet depositories such as Locus Specific databases (LSDBs). Second, diagnostic laboratories would receive no recognition or reward for releasing their data, giving them little incentive to even try.

The Café RouGE approach takes account of the real-world obstacles and the needs of diverse LSDBs (insights provided by GEN2PHEN: http://www.gen2phen.org).

The core concept involves:

• Endowing data analysis tools used by diagnostic laboratories with a ‘data submission’ function that automatically pushes processed data onto the Internet
• Producing a single Internet depot (café) to receive these data and make them available for download by diverse third parties.

The Gensearch® DNA sequence analysis package (PhenoSystems SA) will soon offer this submission functionality, and other tool providers are encouraged to do likewise. We predict that several hundred mutations per month will be released by users of the Gensearch® tool alone.

Cafe Rouge Architecture

Further details of the Cafe Rouge architecture can be found here.

Discuss

Cafe Rouge is currently in its development phase, although the first public release is due in the Autumn. By registering (or logging in via OpenID), you can keep up to date with these development and post comments on the various posts made in the group.

We would also be interested to hear from any individuals/groups who may be interested in using the Cafe Rouge approach as a central clearing house for distributing their biological data. Please email caferouge@gen2phen.org or make a comment/post.