Ontology-based semantic annotation of biomedical data

Clément Jonquet

Stanford Center for Biomedical Informatics Research

24/03/2010 à 10h00

Amphithéatre F107, INRIA Grenoble Rhône-Alpes, Montbonnot Saint-Martin


The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this semantic annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. In this presentation we present both (i) an annotator web service that annotates public datasets with biomedical ontology concepts based on their textual metadata; and (ii) an index of biomedical data annotated with ontology concepts. The annotation workflow used in these two applications uses a concept recognizer to identify concepts in text and a set of semantic expansion components (is_a transitive closure, mappings, semantic distance) to create new annotations. The biomedical community can use our semantic annotation services to tag datasets automatically with ontology terms (from UMLS and NCBO BioPortal ontologies). Such annotations facilitate translational discoveries by integrating annotated data. http://bioportal.bioontology.org/


Dr. Clement Jonquet obtained a PhD in Informatics from University Montpellier 2 http://www.univ-montp2.fr , France in November 2006. Since September 2007, he is a postdoc at the Stanford Center for Biomedical Informatics http://bmir.stanford.edu Research (BMIR) within Pr. Mark A. Musen's group. Dr. Jonquet is currently working on semantic annotations of biomedical data using biomedical ontologies in the context of the National Center for http://www.bioontology.org Biomedical Ontology (NCBO) project. He contributes actively to the design, evolution and development of the NCBO http://bioportal.bioontology.org BioPortal, an ontology web repository widely used in the biomedical informatics community. Dr. Jonquet obtained a BSc, a MSc, and a PhD in Informatics from University Montpellier 2, France. From 2003 to 2006, he had a French government PhD grant and was supervised by Stefano A. Cerri. He worked on multi-agent systems, grid and service-oriented computing in the Laboratory of Informatics, Robotics, and http://www.lirmm.fr Microelectronics of Montpellier (LIRMM), in the Kayou team. From 2003 to 2007, he also worked as a young lecturer and later, as a temporary assistant professor (French Attaché Temporaire d'Enseignement et de Recherche (ATER)) of computer science respectively at University Montpellier 2 and University of Montpellier 3 http://www.univ-montp3.fr. Dr. Jonquet is interested and has experience in several domains such as biomedical informatics, ontology and semantic web, data integration and annotation, distributed systems, agents, service-oriented computing, distant collaboration.

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