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Integrated programming toolkit for common ontology application tasks<br />Tomasz Adamusiak MD PhDtomasz@ebi.ac.uk<br />EBI...
...and no huffing and puffing willblow all of them down...<br />Local ontologies<br />NCBO BioPortal<br />EBI OLS<br /> Le...
EBI Ontology Lookup Service<br />82 ontologies<br />SOAP web services<br />Java client<br />Cote RG, Jones P, Apweiler R, ...
NCBO BioPortal<br />267 ontologies and growing<br />Support for both OWL and OBO<br />REST web services<br />BioPortal Ref...
OLS vs BioPortal (July, 2010)<br />
Integration is hard<br />
OWL API<br />Reference implementation formanipulating and serialising OWL<br />Multiple parsers (inc. OBO)<br />Reasoner i...
It is not a meta-service...<br />OntoCAT database and browser (MOLGENIS)<br />OntoCAT REST service<br />OntoCAT GoogleApp<...
The most important slide ontocat.org<br />?<br />
Where’s my bacon?<br />OntoCAT concept recognizer:<br />http://zooma.sourceforge.net<br />OntoCAT Bioconductor/R package: ...
Google: biomed central ontocat<br />
Acknowledgments<br />Morris A. Swertz’s group at the Genomics Coordination Center (GCC), University of Groningen<br />K Jo...
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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

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

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

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