Research Interests

• Open Biomedical Ontologies
• Knowledge Representation
• Semantic Systems Biology
• The Semantic Web
• The Resource Description Framework (RDF)

Curriculum Vitae

• Birthdate: 14 October, 1979, Deinze, Belgium.
  
  
• 1997 - 2003: MSc. Civil Engineering in Physics, Ghent University
  
  
• 2003 - 2005: MSc. Biomedical and Clinical Engineering Techniques, Ghent University
  
  
• September 2006: Start PhD., Ghent University / VIB
  
  
• January 2009: Continuation PhD., Fac. Bioscience Eng., Ghent University
  
  
• February - May 2009: ESF project, NTNU, Trondheim, Norway
  
  

Research

I do research on Knowledge Management in the biomedical domain. The amount of biological knowledge is very large and it is still growing every day. You can think of all the genes and proteins, from all the different species, with all their interactions, their functions,... This knowledge is integrated in formal, hierarchical and computer readable formats, called ontologies.

A lot of research can be done on these ontologies. How can we query them? How can we present them efficiently? Can we infer new knowlegde from them? How can they integrate in the Semantic Web (the computer understandable internet)? Can we start thinking of making real scientific discoveries within the knowledge contained in ontologies?

In 2007 I developed Metarel, an ontology for relations. It provides metaclasses that are missing in the RO, the Relationship Ontology of the OBO foundry. Metarel is designed to allow the integration of existing OBO relations in its hierarchy.

In spring 2008, I started the development of the RDF Knowledge Base BioGateway, together with Erick Antezana, in the group of Martin Kuiper. I was involved in setting up the specifications for the RDF format and in providing queries for users. As Martin moved to Trondheim, BioGateway was also relocated to Norway and is operational there since the beginning of 2009.

Metarel was integrated in BioGateway from the beginning. In fall 2008, I investigated how it could be exploited to make relational inferences with it. I managed to make many inferences that were intended by the semantics of the OBO relations, with the use of the RDF update language SPARUL.

Ph.D. Advisors:

• Martin Kuiper
  
  
• Bernard De Baets