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OntoCAT - integrated programming toolkit for common ontology application tasks [BOSC2011]
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OntoCAT - integrated programming toolkit for common ontology application tasks [BOSC2011]


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Slides from my talk given at The 12th Annual Bioinformatics Open Source Conference (BOSC 2011), co-located with ISMB/ECCB 2011, Vienna, Austria

Slides from my talk given at The 12th Annual Bioinformatics Open Source Conference (BOSC 2011), co-located with ISMB/ECCB 2011, Vienna, Austria

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  • Three little pigs, an old english fairy tale popularised largely by DisneyLooking at the story from the software point of view the issue here was that the three little pigs did not provide consitent APIs to access their houses. In this context the three little pigs are ontology resources and you the big bad wolf trying to consume them. The problem is they’re build using completetly different technologies, and you need to use different approaches to get to them.
  • Created in VennMaster on July 2010
  • OntoCAT brings semantic web to non-semweb peopleOntoCAT provides a uniform query interface to heterogeneous ontology resources including NCBO BioPortal and EBI Ontology Lookup Service (OLS) as well as local OWL and OBO files. The differences between each resource are wrapped in standard Java and REST services, enabling reuse and integration of ontology software notwithstanding wide variation in underlying technologies. Availability: OntoCAT is available under the LGPLv3 open source
  • Transcript

    • 1. Integrated programming toolkit for common ontology application tasks
      Tomasz Adamusiak MD
      EBI is an Outstation of the European Molecular Biology Laboratory.
    • 2. ...and no huffing and puffing willblow all of them down...
      Local ontologies
      NCBO BioPortal
      EBI OLS
       Leonard Leslie Brooke (1904)
    • 3. EBI Ontology Lookup Service
      82 ontologies
      SOAP web services
      Java client
      Cote RG, Jones P, Apweiler R, Hermjakob H.The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries.BMC Bioinformatics. 2006 Feb 28;7(1):97
    • 4. NCBO BioPortal
      267 ontologies and growing
      Support for both OWL and OBO
      REST web services
      BioPortal Reference Plugin
      Noy, N.F., Shah, N.H., Whetzel, P.L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D.L., Storey, M.A., Chute, C.G., Musen, M.A.BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W170-3.
    • 5. OLS vs BioPortal (July, 2010)
    • 6. Integration is hard
    • 7. OWL API
      Reference implementation formanipulating and serialising OWL
      Multiple parsers (inc. OBO)
      Reasoner interfaces
      Low level API
      Sean Bechhofer, Phillip Lord, Raphael Volz. Cooking the Semantic Web with the OWL API. 2nd International Semantic Web Conference, ISWC, Sanibel Island, Florida, October 2003. PDF
    • 8. It is not a meta-service...
      OntoCAT database and browser (MOLGENIS)
      OntoCAT REST service
      OntoCAT GoogleApp
      ....but could be used to build one
    • 9. The most important slide
    • 10. Where’s my bacon?
      OntoCAT concept recognizer:
      OntoCAT Bioconductor/R package:
    • 11. Google: biomed central ontocat
    • 12. Acknowledgments
      Morris A. Swertz’s group at the Genomics Coordination Center (GCC), University of Groningen
      K Joeri van derVelde
      Dasha Zhernakova
      Helen Parkinson
      Ele Holloway
      Zooma: Tony Burdett
      Bioconductor/R package: Natalja Kurbatova, Pavel Kurnosov, Misha Kapushesky
      EFO: James Malone
      This work was supported by the European Community's Seventh Framework Programmes GEN2PHEN [grant number 200754], SLING [grant number 226073], and SYBARIS [grant number 242220], the European Molecular Biology Laboratory, the Netherlands Organisation for Scientific Research [NWO/Rubicon grant number 825.09.008], and the Netherlands Bioinformatics Centre [BioAssist/Biobanking platform and BioRange grant SP1.2.3]
      OntoCAT logo courtesy of Eamonn Maguire
      Special thanks go to NCBO BioPortal and EBI OLS support teams for all the comprehensive help they provide