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BioCatalogue Presentation @ Enabling Systems Biology 2011, by Jiten Bhagat


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BioCatalogue Presentation @ Enabling Systems Biology 2011, by Jiten Bhagat

  1. 1. JitenBhagatUniversity of<br />ENFIN Enabling Systems Biology 2011<br />April 2011 | London, UK<br /><br />
  2. 2. Agenda<br />2<br />Talk<br />Intro<br />Motivations<br />Core Features<br />Website Demo<br />API<br />Conclusions & Lessons Learned<br />BONUS: iPad Demo <br />by MannieTagarira<br />
  3. 3. The BioCatalogue<br />3<br />A public, centralised and curated registry of Life Science Web Services<br />Allows anyone to register, discover and curate Web Services<br />Community oriented, expert guidance<br />Open content, open source, open platform<br />
  4. 4. Public launch at ISMB 2009 (June 09)<br />4<br />
  5. 5. Reach<br />~18K unique visitors from over 130 countries<br />5<br />
  6. 6. Who<br />6<br />
  7. 7. Motivations (I)<br />Guesstimate 3000+ publicly available online services in Life Sciences<br />Where?<br />can I find them? advertise them?<br />What?<br />do they do? can I use them?<br />the cost? the licenses?<br />How?<br />do they work? up to date?<br />Who?<br />provides them? uses them? <br />recommends them?<br />7<br />
  8. 8. Motivations (II)<br />Discover “Web Services are hard to find”<br />Register “My Web Services are not visible”<br />Annotate “Web Services are poorly described”<br />Monitor “Web Services can be volatile”<br />8<br />
  9. 9. Core Features<br />Web Service registration<br />Annotation<br />descriptions, tags, categories, example data<br />Keyword search<br />Filtering<br />By categories, providers, location, etc<br />Monitoring<br />Checking availability<br />Test scripts<br />9<br />
  10. 10. WEBSITE DEMO<br />10<br />
  11. 11. API<br />11<br />Programmatic access to the BioCatalogue data and features<br />Read & Write APIs<br />Get index of services<br />Search for services<br />Filter services<br />Drill down into the operations / endpoints of a service<br />Register services<br />Submit annotations<br />Follows REST principles (XML & JSON outputs)<br />
  12. 12. NCRI ONIX Resource Catalogue<br />12<br />
  13. 13. BioCatalogue in Taverna<br />ISMB 10<br />13<br />
  14. 14. Mass Curation Tool<br />To aid the curation of Web Services via the use of spreadsheets<br />Uses the BioCatalogue’s API<br />Desktop application<br />Browse/Search the BioCatalogue<br />Export to an Excel Spreadsheet<br />Annotate<br />Submit annotations to the BioCatalogue<br />14<br />
  15. 15. Mass Curation Tool<br />15<br />ISMB 10<br />
  16. 16. Apps - Coming Soon<br />13th April 2011<br />ENFIN Enabling Systems Biology 2011<br />16<br />iPad app (exclusive demo after this)<br />Android app<br />myExperiment integration<br />
  17. 17. EdUnify Registry<br />ISMB 10<br />17<br /> - Web Services for Education<br /><br />
  18. 18. Some Lessons Learnt<br />Describing Web Services is HARD<br />We need to provide comprehensive APIs to the registry<br />The SOAP/REST technical view over services is not enough<br />Need a more functional / task-oriented view<br />18<br />
  19. 19. How Can You Get Involved?<br />Join in the curation of Web Services<br />Describe how they work<br />Provide examples<br />Tag and categorise<br />Join in the development of the software<br />Build applications / integrate using the API<br />Install your own BioCatalogue instance<br />Provide feedback and suggestions<br />19<br />
  20. 20. Acknowledgements<br />Rodrigo Lopez<br />Eric Nzuobontane <br />Thomas Laurent<br />Hamish McWilliams<br />Carole Goble<br />David De Roure<br />JitenBhagat<br />Katy Wolstencroft<br />Franck Tanoh<br />Steve Pettifer<br />Robert Stevens<br />20<br />SergejsAleksejevs<br />MannieTagarira<br />JerzyOrlowski<br />
  21. 21.
  22. 22. Thank You<br />Over to Mannie…<br /><br />About Us -<br />API Docs -<br />22<br />Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S., Lopez, R., Goble, C.A.: BioCatalogue: a universal catalogue of web services for the life sciences, Nucl. Acids Res., 2010. doi:10.1093/nar/gkq394<br />