Applying ontologies to biomedical data; views, rules and annotation tools


In this webinar we will present some of the issues and challenges we face in building a scalable, ontology based annotation platform. Annotating biological data with ontologies offers many exciting possibilities for data integration and analysis. The wealth of biomedical ontologies now available (5.5M terms in BioPortal alone) means it is becoming increasingly difficult to effectively organise and present relevant subsets of these ontologies to the various communities and applications that seek to exploit them. These issues range from simple concerns relating to which terms, labels or portions of hierarchy should be exposed, to more complicated issues such as exporting relevant logical subsets or modules from the ontologies.

In exploring how to build our annotation platform, we will discuss strategies for tailoring subsets of ontologies to specific types of data and show how these views can be utilised in external applications. We will also present some tools that help us reduce the ontology development bottleneck and enable the biologists to play a more active role in an ontology's evolution.

Simon Jupp is a bioinformatician working in the functional genomics group at the European Bioinformatics Institute. Simon has a special interest in the development of OWL ontologies and the Semantic Web. Simon previously worked on the EU SeaLife and e-LICO projects at the Bio-Health Informatics Group, University of Manchester, where his research was primarily focused on exploring Semantic Web technologies for the life sciences.  Simon has a bachelors degree in Biochemistry and a masters degree in Computer Science both from the University of Wales, Aberystwyth.