View
214
Download
0
Category
Tags:
Preview:
Citation preview
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)
0
2
4
6
8
10
12
14
Num
ber
of E
ntrie
s S
ubm
itted
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
Recommended