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Sanger Mouse
 Resources Portal
A Testbed for Collaborative Data Integration


         Darren Oakley, Vivek Iyer, Bill Ska...
Making a
Collaborative Data
     Portal...
‘Borg’ Approach

         •   Single group becomes
             sole owner/curator of
             portal and its data

  ...
burp
Why This Works


•   Clearly defined centre

•   It provides central curation for all data
Mouse Informatics

    •   Genes

        •   Mutants (ES Cells, Mice)

            •   Phenotypes

•   In mouse informati...
Mouse Informatics

•   Times are changing...

    •   Other informatics groups are providing
        high volume data and ...
“Hand over your data,
prepare to be assimilated”




                                                                “No, ...
“Hand over your data,
prepare to be assimilated”




                                                                     ...
‘Federation’ Approach
            •   Each group hosts
                their own data and
                exposes it via d...
The Sanger Mouse
 Resources Portal
 http://www.sanger.ac.uk/mouseportal

(Our Attempt at the Federation Approach...)
Distributed Data
•   Currently 5 distinct, but related sets of
    mouse data:

    •   Gene Information

    •   Phenotyp...
Screenshot Tour
Technologies
Search Engine
                Portal Interface



Data Services
index searchable
     terms
index searchable
     terms
MartSearch / Portal




index searchable
     terms
MartSearch / Portal


send users search term to Solr




index searchable
     terms
MartSearch / Portal


send users search term to Solr

     Solr returns groups of terms
    to query Biomarts with




ind...
MartSearch / Portal


send users search term to Solr

     Solr returns groups of terms
    to query Biomarts with
       ...
User searches for ‘Cbx7’
User searches for ‘Cbx7’


     Search for ‘Cbx7’
User searches for ‘Cbx7’


     Search for ‘Cbx7’
     JSON data containing information on
     what to search each biomar...
User searches for ‘Cbx7’


     Search for ‘Cbx7’
     JSON data containing information on
     what to search each biomar...
User searches for ‘Cbx7’


     Search for ‘Cbx7’
     JSON data containing information on
     what to search each biomar...
Extending The Portal

•   Put new data into a Biomart

•   Write JSON config file for MartSearch
    (defining filters to ...
Advantages


•   Easily extensible

•   Data responsibility shared
Disadvantages

•   Hard to avoid redundancy

    •   Sometimes needed for data linking

•   Un-curated

    •   Each group...
Disclaimer
•   Windows users...

    •   If you use IE - it will eat your browser

    •   Use Firefox/Chrome/Safari/Opera...
Acknowledgments
•   Funding: I-DCC grant (EU FP7)

    •   Coordination of informatic resources
        from high-throughp...
http://www.sanger.ac.uk/mouseportal

http://github.com/dazoakley/martsearch

do2@sanger.ac.uk

dazoakley
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration
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The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration

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A brief overview of how we put the new Sanger mouse portal together.

This presentation was given at the International Workshop for Portals in Life Sciences (IWPLS) 14th September 2009, Edinburgh.

Published in: Technology, Business
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Transcript of "The Sanger Mouse Resources Portal - A Testbed for Collaborative Data Integration"

  1. 1. Sanger Mouse Resources Portal A Testbed for Collaborative Data Integration Darren Oakley, Vivek Iyer, Bill Skarnes
  2. 2. Making a Collaborative Data Portal...
  3. 3. ‘Borg’ Approach • Single group becomes sole owner/curator of portal and its data • Other groups feed their data into portal group
  4. 4. burp
  5. 5. Why This Works • Clearly defined centre • It provides central curation for all data
  6. 6. Mouse Informatics • Genes • Mutants (ES Cells, Mice) • Phenotypes • In mouse informatics, the traditional Borg is MGI - this has worked nicely for many years: http://informatics.jax.org
  7. 7. Mouse Informatics • Times are changing... • Other informatics groups are providing high volume data and want in on the portal game
  8. 8. “Hand over your data, prepare to be assimilated” “No, YOU hand over your data and prepare to be assimilated” “Ahem, both of you, prepare to be assimilated!”
  9. 9. “Hand over your data, prepare to be assimilated” “No, YOU hand over your data and prepare to be assimilated” ? lB org he rea t yo u is c h of … whi “Ahem, both of you, prepare to be assimilated!”
  10. 10. ‘Federation’ Approach • Each group hosts their own data and exposes it via defined services • Make a ‘clever’ portal that pulls of these resources together • No single group is totally in charge
  11. 11. The Sanger Mouse Resources Portal http://www.sanger.ac.uk/mouseportal (Our Attempt at the Federation Approach...)
  12. 12. Distributed Data • Currently 5 distinct, but related sets of mouse data: • Gene Information • Phenotyping • Mutant Mouse Breeding • Mutant ES Cell / Vector Production • Other DNA Resources
  13. 13. Screenshot Tour
  14. 14. Technologies Search Engine Portal Interface Data Services
  15. 15. index searchable terms
  16. 16. index searchable terms
  17. 17. MartSearch / Portal index searchable terms
  18. 18. MartSearch / Portal send users search term to Solr index searchable terms
  19. 19. MartSearch / Portal send users search term to Solr Solr returns groups of terms to query Biomarts with index searchable terms
  20. 20. MartSearch / Portal send users search term to Solr Solr returns groups of terms to query Biomarts with send asynchronous requests to each of the Biomarts for the data the user is interested in index searchable terms
  21. 21. User searches for ‘Cbx7’
  22. 22. User searches for ‘Cbx7’ Search for ‘Cbx7’
  23. 23. User searches for ‘Cbx7’ Search for ‘Cbx7’ JSON data containing information on what to search each biomart by...
  24. 24. User searches for ‘Cbx7’ Search for ‘Cbx7’ JSON data containing information on what to search each biomart by... Search using query parameters defined by Solr response
  25. 25. User searches for ‘Cbx7’ Search for ‘Cbx7’ JSON data containing information on what to search each biomart by... Search using query parameters defined by Solr response Render search results using templates
  26. 26. Extending The Portal • Put new data into a Biomart • Write JSON config file for MartSearch (defining filters to index and use) • Rebuild the index
  27. 27. Advantages • Easily extensible • Data responsibility shared
  28. 28. Disadvantages • Hard to avoid redundancy • Sometimes needed for data linking • Un-curated • Each group can curate its own data • No curation as a whole
  29. 29. Disclaimer • Windows users... • If you use IE - it will eat your browser • Use Firefox/Chrome/Safari/Opera for a more pleasant internet experience • We are working on it - IE 8 gives an ok experience...
  30. 30. Acknowledgments • Funding: I-DCC grant (EU FP7) • Coordination of informatic resources from high-throughput mouse ES cell mutagensis programs • Wellcome Trust Sanger Institute • T87 - ES Cell Mutagenesis • MIG - Mouse Informatics Group
  31. 31. http://www.sanger.ac.uk/mouseportal http://github.com/dazoakley/martsearch do2@sanger.ac.uk dazoakley

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