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Café for Routine Genetic Data Exchange (Café RouGE) Human Variome Project Meeting, Paris 2010 Dr Owen Lancaster.

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Presentation on theme: "Café for Routine Genetic Data Exchange (Café RouGE) Human Variome Project Meeting, Paris 2010 Dr Owen Lancaster."— Presentation transcript:

1 Café for Routine Genetic Data Exchange (Café RouGE) Human Variome Project Meeting, Paris 2010 Dr Owen Lancaster

2 Core Concept Produce a single Internet conduit/depot (café) to receive diagnostic lab data, and make them available for download by diverse third parties

3 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

4 Standard format(s) Not a database ‘MENU’/’SHOP WINDOW’/’CONDUIT’/’HUB’ Aims to help the flow of data: Diagnostic labs -> 3 rd parties Café RouGE Overview Diagnostic labs using “Café RouGE enabled” DNA diagnostic software e.g. Gensearch (PhenoSystems) Diverse third parties wishing to access data e.g. LSDBs

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

6 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

7 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, 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

8 Create entry with HTTP POST Update entry with HTTP PUT Retrieve entry with HTTP GET Update entry with HTTP PUT Delete 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 Retrieve entry with HTTP GET Create entry with HTTP POST 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

9 Discovering/accessing mutation data in GEN2PHEN Knowledge Centre

10 Managing mutation data via the central Café RouGE web application

11 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) Number of Entries Submitted

12 3 rd 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 3 rd party tools welcome to access Café RouGE API to pull in data

13 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

14 Acknowledgements Anthony Brookes, David Atlan, Gudmundur Thorisson, Adam Webb, Rob Free, Raymond Dalgleish Co-workers in Brookes Group, University of Leicester Owen Lancaster The research leading to these results has received funding from the European Community’s Seventh Framework Programme (FP7/ ) under grant agreement n – the GEN2PHEN project


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