http://www.caferouge.org

Café for Routine Genetic Data Exchange(Café RouGE)

Human Variome Project Meeting, Paris 2010

Dr Owen Lancaster

Core Concept

Produce a single Internet conduit/depot (café) to receive diagnostic lab data, and make them

available for download by diverse third parties

Why?

• Diagnostic laboratory personnel do not have time nor funding to manually submit data to internet depositories such as Locus Specific databases– Submission can be a real chore

• Diagnostic laboratories would receive no recognition or reward for releasing their data• Hence little incentive to try

• Diagnostic laboratories are willing to submit• Need a simple automated way to achieve this

Standard format(s)

Not a database‘MENU’/’SHOP WINDOW’/’CONDUIT’/’HUB’

Aims to help the flow of data:Diagnostic labs -> 3rd parties

Café RouGE OverviewDiagnostic labs using “Café RouGE enabled” DNA diagnostic software e.g. Gensearch (PhenoSystems)

Diverse third parties wishing to access data e.g. LSDBs

“Café RouGE Enabled” Gensearch DNA analysis tool (PhenoSystems)

“Café RouGE Enabled” Gensearch DNA analysis tool

Café RouGE Features

• View “menu” of mutation datasets through GEN2PHEN Knowledge Centre– Subscribe to alerts (feeds) of interest (specific gene etc)– Request access to non-public datasets

• Submitter data management web application– Delete entries, configure access levels

(public/metadata/private)

• Bundling of optional supporting primary data (e.g. chromatograms)

• Aggregating information on who is submitting and using data, so that reliable and transparent micro-attribution can be enabled

• Managing data submission and access via digital IDs for system users

Café RouGE Architecture• Data submitted to Café RouGE as web feed entries

– A web feed is a simple XML document describing a collection of items, typically blog entries or news headlines or any list of items

– Subscribe to feeds using software (e.g. Google Reader, email clients) to receive updates published on websites

– Atom Syndication Format is a popular, extensible feed format and is used as the format of variants in Café Rouge

• Assign categories to data to make it more manageable

– Allows picking and choosing of data for users (e.g. LSDB curator for specific gene)

• Café RouGE is built around AtomServer - a generic, off-the-shelf open-source Atom data store and uses standard web protocols

Create entry with HTTP POST

Update entry with HTTP PUT

Retrieve entry with HTTP GET

Update entry with HTTP PUTDelete entry with HTTP DELETE

Data uploaded via webservice using a simple, standard operation

Submitting mutation data from diagnostic lab using “Café RouGE enabled” software e.g. Gensearch (Phenosystems)

Discovering/accessing mutation feeds in GEN2PHEN Knowledge Centre or via other third party tools

Retriev

e entry

with

HTT

P GET

Create entry w

ith HTTP POST

The Café RouGE approach could be applied to distributing other types of biological data, e.g. genotypes, NGS, CNVs

The Café RouGE approach could be applied to distributing other types of biological data, e.g. genotypes, NGS, CNVs

Entries are manipulated with simple, standard operations

Managing mutation data via the central Café RouGE web application

AtomServer data store

Central mutation depot

Discovering/accessing mutation data in GEN2PHEN Knowledge Centre

Managing mutation data via the central Café RouGE web application

Pilot Study Submissions

• 65 variant entries submitted from pilot diagnostic lab using “Café RouGE enabled” Gensearch software (PhenoSystems)– 29 genes total between mid-Feb and start of April

• Will soon deploy to other users of Gensearch tool (~100 installs)

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3rd Parties Accessing Café RouGE

• Developing Café RouGE plugin/integration for LOVD– Allow LSDB curators to check Café RouGE hub

for data for their gene of interest– Import into their database

• Currently under development

• Will be piloting in coming months

• Other 3rd party tools welcome to access Café RouGE API to pull in data

Get Involved with Café RouGE

• Open access to Café RouGE API for developers/users of third parties/tools

• Encouraging DNA diagnostic tool providers to produce Cafe Rouge enabled versions of software

• Diagnostic laboratories wishing to submit their data– Can accept data dumps for analysis tools which

currently have no Café RouGE submit function

• Please contact if interested– ol8@le.ac.uk

Acknowledgements

• Anthony Brookes, David Atlan, Gudmundur Thorisson, Adam Webb, Rob Free, Raymond Dalgleish

• Co-workers in Brookes Group, University of Leicester

Owen Lancaster (ol8@le.ac.uk)

The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement n 200754 – the GEN2PHEN project