BioCatalogue Presentation @ Enabling Systems Biology 2011, by Jiten Bhagat
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  • Stats, uptake, usage, since Launch
  • Make sure to explain why annotation is HARD
  • Infrastructure is not biology specific

BioCatalogue Presentation @ Enabling Systems Biology 2011, by Jiten Bhagat BioCatalogue Presentation @ Enabling Systems Biology 2011, by Jiten Bhagat Presentation Transcript

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