G03-SemanticWeb-OntoCAT

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  • Created in VennMaster on July 2010
  • G03-SemanticWeb-OntoCAT

    1. 1. Tomasz Adamusiak MD PhD [email_address] Integrated programming toolkit for common ontology application tasks EBI is an Outstation of the European Molecular Biology Laboratory.
    2. 2. ...and no huffing and puffing will blow all of them down... <ul><li>Local ontologies </li></ul><ul><li>NCBO BioPortal </li></ul><ul><li>EBI OLS </li></ul>  Leonard Leslie Brooke (1904)
    3. 3. EBI Ontology Lookup Service <ul><li>82 ontologies </li></ul><ul><li>SOAP web services </li></ul><ul><li>Java client </li></ul><ul><li>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 </li></ul>
    4. 4. NCBO BioPortal <ul><li>267 ontologies and growing </li></ul><ul><li>Support for both OWL and OBO </li></ul><ul><li>REST web services </li></ul><ul><li>BioPortal Reference Plugin </li></ul><ul><li>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. </li></ul>
    5. 5. OLS vs BioPortal (July, 2010)
    6. 6. INTEGRATION IS HARD
    7. 7. OWL API <ul><li>Reference implementation for manipulating and serialising  OWL </li></ul><ul><li>Multiple parsers (inc. OBO) </li></ul><ul><li>Reasoner interfaces </li></ul><ul><li>Low level API </li></ul><ul><li>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 </li></ul>
    8. 8. It is not a meta-service... <ul><li>OntoCAT database and browser (MOLGENIS) </li></ul><ul><li>OntoCAT REST service </li></ul><ul><li>OntoCAT GoogleApp </li></ul>....but could be used to build one
    9. 9. The most important slide ontocat.org searchAll() searchOntology() getChildren() getParents() getSynonyms() getDefinitions() getParents() ...
    10. 10. Where’s my bacon? <ul><li>OntoCAT concept recognizer : </li></ul><ul><ul><li>http://zooma.sourceforge.net </li></ul></ul><ul><li>OntoCAT Bioconductor/R package : </li></ul><ul><ul><li>http://www.ontocat.org/wiki/r </li></ul></ul>
    11. 11. Google: biomed central ontocat
    12. 12. Acknowledgments <ul><li>Morris A. Swertz ’s group at the G enomics Coordination Center (GCC) , University of Groningen </li></ul><ul><ul><li>K Joeri van der Velde </li></ul></ul><ul><ul><li>Despoina Antonakaki </li></ul></ul><ul><ul><li>Dasha Zhernakova </li></ul></ul><ul><li>Helen Parkinson </li></ul><ul><li>Niran Abeygunawardena </li></ul><ul><li>Ele Holloway </li></ul><ul><li>Zooma : Tony Burdett </li></ul><ul><li>Bioconductor/R package : Natalja Kurbatova, Pavel Kurnosov, Misha Kapushesky </li></ul><ul><li>EFO : James Malone </li></ul>Special thanks go to NCBO BioPortal and EBI OLS support teams for all the comprehensive help they provide OntoCAT logo courtesy of Eamonn Maguire 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]

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