July 22, 2011: Compbio Invited Talk - Catia Pesquita: "Auxesia: Semi-automated Ontology Extension"

Compbio Invited Talk

Auxesia: Semi-automated Ontology Extension

Catia Pesquita
University of Lisbon
Friday, July 22, 2011
12:30 PM - 02:00 PM, 1325 SEO Building


Biomedical ontologies are crucial for bridging the gap between biomedical data and biomedical knowledge, since they provide a structured and unambiguous model of the concepts needed to understand a domain. Developing and maintaining a biomedical ontology is a time and effort-consuming task, given the dynamic and expanding nature of biomedical knowledge. This is a relevant issue for very large ontologies which cover a broad domain, for smaller ontologies maintained by a small team and also for domains where being able to perform quick updates is critical (e.g. epidemiology).?To help minimize this effort, we can capitalize on ontology engineering methods, such as ontology learning and ontology matching, to provide new candidate concepts for a biomedical ontology, and thus extend it.

I am developing a methodology for semi-automated ontology extension, called Auxesia, which aims at addressing two of the biggest issues when working with biomedical ontologies: their size and the complexity of their terminology. To cope with these Auxesia explores two main sources of knowledge, other biomedical ontologies and scientific publications, by applying on one hand ontology matching and on the other text mining. It also incorporates a novel methodology for predicting the areas of the ontology which would benefit the most from extension, thereby focusing the extension effort.


Catia Pesquita?is a PhD Candidate in Computer Science (Bioinformatics) at the Faculty of Sciences of the University of Lisbon focused on Automated Extension of Biomedical Ontologies under the supervision of Francisco Couto. She is a member of Lasige at the XLDB group, where she is involved in the following projects: BOA (BioOntologies Applications), AEB and VPH-NoE. She has an MSc in Bioinformatics (2008) and a degree in Cell Biology and Biotechnology (2005). Her research interests include Biomedical Ontologies, Semantic Similarity, Ontology Evolution, Knowledge Management and Data and Text Mining. She is visiting the ADVIS Lab directed by Isabel Cruz in the summer of 2011. She is making the most of her visit by also interacting with the Compbio Lab directed by Tanya Berger-Wolf and the Creative Algorithms Lab directed by Bhaskar DasGupta.

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