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Café for Rou tine G enetic Data E xchange (Café RouGE )

Café for Rou tine G enetic Data E xchange (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 ?.

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Café for Rou tine G enetic Data E xchange (Café RouGE )

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

  5. “CaféRouGE Enabled” Gensearch DNA analysis tool “CaféRouGE Enabled” GensearchDNA analysis tool (PhenoSystems)

  6. Café RouGEFeatures • 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. CaféRouGE 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

  8. Data uploaded via webservice using a simple, standard operation Retrieve entry with HTTP GET 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 Update entry with HTTP PUT Create entry with HTTP POST Update entry with HTTP PUT Retrieve entry with HTTP GET Delete entry with HTTP DELETE Create entry with HTTP POST AtomServer data store Central mutation depot The CaféRouGE 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 CaféRouGE web application

  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 “CaféRouGE 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. 3rd Parties Accessing CaféRouGE • Developing CaféRouGEplugin/integration for LOVD • Allow LSDB curators to check CaféRouGE 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 CaféRouGE API to pull in data

  13. Get Involved with CaféRouGE • Open access to CaféRouGE 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 CaféRouGE submit function • Please contact if interested • ol8@le.ac.uk

  14. Acknowledgements • Anthony Brookes, David Atlan,GudmundurThorisson, 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

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