EBI is an Outstation of the European Molecular Biology Laboratory.

Tomasz Adamusiak MD PhD

tomasz@ebi.ac.uk

Integrated programming toolkit for common ontology

application tasks

EBI is an Outstation of the European Molecular Biology Laboratory.

...and no huffing and puffing willblow all of them down...

Local ontologies

NCBO BioPortal

EBI OLS

Leonard Leslie Brooke (1904)

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

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.

OLS vs BioPortal (July, 2010)

INTEGRATION IS HARD

OWL API

• Reference implementation for manipulating 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

It is not a meta-service...

OntoCAT database and browser (MOLGENIS)

OntoCAT REST service

OntoCAT GoogleApp

....but could be used to build one

The most important slide ontocat.org

searchAll()

searchOntology()

getChildren()

getParents()

getSynonyms()

getDefinitions()

getParents()...

Where’s my bacon?

• OntoCAT concept recognizer:• http://zooma.sourceforge.net

• OntoCAT Bioconductor/R package: • http://www.ontocat.org/wiki/r

Google: biomed central ontocat

Acknowledgments

• Morris A. Swertz’s group at the Genomics Coordination Center (GCC), University of Groningen

• K Joeri van der Velde• Despoina Antonakaki• Dasha Zhernakova

• Helen Parkinson• Niran Abeygunawardena• Ele Holloway

• Zooma: Tony Burdett

• Bioconductor/R package: Natalja Kurbatova, Pavel Kurnosov, Misha Kapushesky

• EFO: James Malone 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]