ISMB 2010 BioCatalogue presentation


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The slides were presented by Jiten Bhagat at ISMB 2010 in Boston (US)

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  • Launched about a year ago. We’ll give you an update on what we have done since.
  • University of Manchester, UK European Bioinformatics Institute based in Cambridge, UK
  • We’ve built a catalogue for all of this… Cost Licensing
  • Stats, uptake, usage
  • Stats, uptake, usage, since Launch
  • Stats, uptake, usage, since Launch
  • Make sure to explain why annotation is HARD
  • Infrastructure is not biology specific
  • Missing rory, tom and scott and finn and mannie
  • ISMB 2010 BioCatalogue presentation

    1. 1. Jiten Bhagat University of Manchester [email_address] ISMB 2010 July 2010 | Boston, MA USA
    2. 2. <ul><li>A public centralised and curated registry of Life Science Web Services </li></ul><ul><li>‘ Web 2.0’-style website and API </li></ul><ul><li>Allow anyone to register, discover and curate Web Services </li></ul><ul><li>Community oriented with expert guidance </li></ul><ul><li>Open content, open source, open platform </li></ul>11th July 2010 ISMB 10
    3. 3. Public launched a year ago at ISMB 2009 11th July 2010 ISMB 10
    4. 4. Who 11th July 2010 ISMB 10
    5. 5. Revisiting the Motivations (I) <ul><li>Guesstimate 3000+ publicly available online services in Life Sciences </li></ul><ul><li>Where? </li></ul><ul><ul><li>can I find them? advertise them? </li></ul></ul><ul><li>What? </li></ul><ul><li>do they do? can I use them? </li></ul><ul><li>the cost? the licenses? </li></ul><ul><li>How? </li></ul><ul><li>do they work? up to date? </li></ul><ul><li>Who? </li></ul><ul><li>provides them? uses them? </li></ul><ul><li>recommends them? </li></ul>11th July 2010 ISMB 10
    6. 6. Revisiting the Motivations (II) <ul><li>Discover “Web Services are hard to find” </li></ul><ul><li>Register “My Web Services are not visible” </li></ul><ul><li>Annotate “Web Services are poorly described” </li></ul><ul><li>Monitor “Web Services can be volatile” </li></ul>11th July 2010 ISMB 10
    7. 7. Where Are We Now <ul><li>Project is active and going strong </li></ul><ul><li>Building up content and metadata </li></ul><ul><li>Constant, iterative development and releases </li></ul><ul><li>Full time curator with a focus group of users </li></ul><ul><li>Active community involvement & outreach </li></ul>11th July 2010 ISMB 10
    8. 8. Reach <ul><li>11K unique visitors from over 120 countries </li></ul>11th July 2010 ISMB 10
    9. 9. Stats <ul><li>390+ registered members </li></ul><ul><li>120+ service providers </li></ul><ul><li>1.7K Web Services with over 11K SOAP operations and 1K REST endpoints </li></ul><ul><li>Almost 50K annotations </li></ul><ul><ul><li>33K from providers (and WSDL docs) </li></ul></ul><ul><ul><li>9K from users </li></ul></ul>11th July 2010 ISMB 10
    10. 10. Started With... <ul><li>Simple Web Service registration </li></ul><ul><li>Annotation </li></ul><ul><ul><li>Descriptions, Tags, Categories, Example Data </li></ul></ul><ul><li>Keyword search </li></ul><ul><li>Filtering </li></ul><ul><li>Basic monitoring </li></ul>11th July 2010 ISMB 10
    11. 11. Now (I) <ul><li>Features and Improvements </li></ul><ul><ul><li>Brand new more &quot;active&quot; homepage </li></ul></ul><ul><ul><li>More monitoring features </li></ul></ul><ul><ul><ul><li>EMBRACE test scripts </li></ul></ul></ul><ul><ul><li>Automatic service update checker </li></ul></ul><ul><ul><li>Better support for describing REST services </li></ul></ul><ul><ul><li>More annotation fields for metadata </li></ul></ul><ul><ul><li>Activity feeds & monitoring status changes </li></ul></ul><ul><ul><li>Improved website interface </li></ul></ul>11th July 2010 ISMB 10
    12. 12. Now (II) <ul><li>Programmatic access to the BioCatalogue data and features (API) </li></ul><ul><ul><li>Read only </li></ul></ul><ul><ul><ul><li>Write API coming soon </li></ul></ul></ul><ul><ul><li>Used in: </li></ul></ul><ul><ul><ul><li>NCRI's ONIX platform </li></ul></ul></ul><ul><ul><ul><li>Taverna plugin </li></ul></ul></ul><ul><ul><ul><li>BioCatalogue Mass Curation app (using spreadsheets) </li></ul></ul></ul><ul><ul><ul><li>myExperiment integration </li></ul></ul></ul><ul><ul><li>Follows REST principles (XML & JSON outputs) </li></ul></ul>11th July 2010 ISMB 10
    13. 13. Now (II) <ul><li>Content Acquisition, Outreach & Papers </li></ul><ul><ul><li>Merged the data from the EMBRACE registry </li></ul></ul><ul><ul><li>NAR paper published (featured in top 5%) </li></ul></ul><ul><ul><li>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 </li></ul></ul><ul><ul><li>Annotation jamboree with 15 folks </li></ul></ul><ul><ul><ul><li>Providers and consumers </li></ul></ul></ul><ul><ul><li>Presentations and posters at events </li></ul></ul>11th July 2010 ISMB 10
    14. 14. DEMO 11th July 2010 ISMB 10
    15. 15. NCRI ONIX Resource Catalogue 11th July 2010 ISMB 10
    16. 16. BioCatalogue in Taverna 11th July 2010 ISMB 10
    17. 17. Mass Curation Tool <ul><li>To aid the curation of Web Services via the use of spreadsheets </li></ul><ul><li>Uses the BioCatalogue’s API </li></ul><ul><li>Desktop application </li></ul><ul><ul><li>Browse/Search the BioCatalogue </li></ul></ul><ul><ul><li>Export to an Excel Spreadsheet </li></ul></ul><ul><ul><li>Annotate </li></ul></ul><ul><ul><li>Submit annotations to the BioCatalogue </li></ul></ul>11th July 2010 ISMB 10
    18. 18. Mass Curation Tool 11th July 2010 ISMB 10
    19. 19. EdUnify Registry 11th July 2010 ISMB 10 - Web Services for Education
    20. 20. Some Lessons Learnt <ul><li>Describing Web Services is HARD </li></ul><ul><li>We need to provide comprehensive APIs to the registry </li></ul><ul><li>The SOAP/REST technical view over services is not enough </li></ul><ul><ul><li>Need a more functional / task-oriented view </li></ul></ul>11th July 2010 ISMB 10
    21. 21. Where We’re Heading <ul><li>Functional Units </li></ul><ul><ul><li>What tasks/functionality does this Web Service provide? </li></ul></ul><ul><li>Testing services directly on the BioCatalogue </li></ul><ul><li>Better support for developers </li></ul><ul><ul><li>Both for the BioCatalogue codebase and API use </li></ul></ul><ul><li>Carrying on with curation and community building </li></ul>11th July 2010 ISMB 10
    22. 22. How Can You Get Involved? <ul><li>Join in the curation of Web Services </li></ul><ul><ul><li>Describe how they work </li></ul></ul><ul><ul><li>Tag and categorise </li></ul></ul><ul><li>Join in the development of the software </li></ul><ul><li>Build applications / integrate using the API </li></ul><ul><li>Install your own BioCatalogue instance </li></ul><ul><li>Provide feedback and suggestions </li></ul>11th July 2010 ISMB 10
    23. 23. Acknowledgements Thomas Laurent Hamish McWilliams Franck Tanoh Jiten Bhagat Carole Goble Steve Pettifer Katy Wolstencroft Robert Stevens David De Roure 11th July 2010 ISMB 10 Mannie Tagarira Rodrigo Lopez Eric Nzuobontane
    24. 25. Thank You About Us - API Docs - 11th July 2010 ISMB 10 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