OntoCAT - integrated programming toolkit for common ontology application tasks [BOSC2011]
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![Integrated programming toolkit for common ontology application tasks,[object Object],Tomasz Adamusiak MD PhDtomasz@ebi.ac.uk,[object Object],EBI is an Outstation of the European Molecular Biology Laboratory. ,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-1-2048.jpg?cb=1668150277)
![...and no huffing and puffing willblow all of them down...,[object Object],Local ontologies,[object Object],NCBO BioPortal,[object Object],EBI OLS,[object Object], Leonard Leslie Brooke (1904),[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-2-2048.jpg?cb=1668150277)
![EBI Ontology Lookup Service,[object Object],82 ontologies,[object Object],SOAP web services,[object Object],Java client,[object Object],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,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-3-2048.jpg?cb=1668150277)
![NCBO BioPortal,[object Object],267 ontologies and growing,[object Object],Support for both OWL and OBO,[object Object],REST web services,[object Object],BioPortal Reference Plugin,[object Object],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.,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-4-2048.jpg?cb=1668150277)
![OLS vs BioPortal (July, 2010),[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-5-2048.jpg?cb=1668150277)
![Integration is hard,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-6-2048.jpg?cb=1668150277)
![OWL API,[object Object],Reference implementation formanipulating and serialising OWL,[object Object],Multiple parsers (inc. OBO),[object Object],Reasoner interfaces,[object Object],Low level API,[object Object],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,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-7-2048.jpg?cb=1668150277)
![It is not a meta-service...,[object Object],OntoCAT database and browser (MOLGENIS),[object Object],OntoCAT REST service,[object Object],OntoCAT GoogleApp,[object Object],....but could be used to build one,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-8-2048.jpg?cb=1668150277)
![The most important slide ontocat.org,[object Object],?,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-9-2048.jpg?cb=1668150277)
![Where’s my bacon?,[object Object],OntoCAT concept recognizer:,[object Object],http://zooma.sourceforge.net,[object Object],OntoCAT Bioconductor/R package: ,[object Object],http://www.ontocat.org/wiki/r,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-10-2048.jpg?cb=1668150277)
![Google: biomed central ontocat,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-11-2048.jpg?cb=1668150277)
![Acknowledgments,[object Object],Morris A. Swertz’s group at the Genomics Coordination Center (GCC), University of Groningen,[object Object],K Joeri van derVelde,[object Object],DespoinaAntonakaki,[object Object],Dasha Zhernakova,[object Object],Helen Parkinson,[object Object],NiranAbeygunawardena,[object Object],Ele Holloway,[object Object],Zooma: Tony Burdett,[object Object],Bioconductor/R package: Natalja Kurbatova, Pavel Kurnosov, Misha Kapushesky,[object Object],EFO: James Malone,[object Object],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],[object Object],OntoCAT logo courtesy of Eamonn Maguire,[object Object],Special thanks go to NCBO BioPortal and EBI OLS support teams for all the comprehensive help they provide,[object Object]](https://image.slidesharecdn.com/slideshareadamusiakbosc2011ontocat-110717052323-phpapp01/75/ontocat-integrated-programming-toolkit-for-common-ontology-application-tasks-bosc2011-12-2048.jpg?cb=1668150277)
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]
Editor's Notes
- 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