Foundation Medicine



IO Informatics

Conference on Semantics in Healthcare and Life Sciences

Keynote Speaker - Dr. Olivier Bodenreider

Chief, Cognitive Science Branch
National Library of Medicine
National Institutes of Health
Bethesda, MD, United States

Presentation Title:
From Biomedical Information Integration to Knowledge Discovery Through the Semantic Web

Presentation (pdf)

Abstract:  Over the past decade, knowledge resources have become increasingly available not only for humans to read and make sense of, but also electronically, which make these data amenable to automated processing. Structured knowledge sources have been developed and integrated in systems such as Entrez, developed by the National Center for Biotechnology Information (NCBI). Vast amounts of biomedical text have also been processed in order to extract entities and relations. In the clinical domain, data warehouses created from electronic health record systems have been created in virtually every institution involved in translational research. Finally, the biomedical domain is rich of many ontologies, which provide the vocabulary for normalizing entities and relationships in these knowledge sources, as well as the domain knowledge to interpret the content of these resources. Semantic Web technologies have emerged as the infrastructure of choice for integrating biomedical information.
This talk will focus on the experimental Biomedical Knowledge Repository being developed at the National Library of Medicine. This repository leverages Semantic Web technologies to integrate the Unified Medical Language System (UMLS), 60 M relations extracted from PubMed/MEDLINE abstracts by the SemRep natural language processing (NLP) system, as well as features from Entrez Gene. We will show how definitional knowledge from biomedical ontologies can complement assertional knowledge extracted from the literature in support of hypothesis generation and knowledge discovery.

Biography:  Olivier Bodenreider is a Senior Scientist and Chief of the Cognitive Science Branch of the Lister Hill National Center for Biomedical Communications at the US National Library of Medicine.

His research focuses on terminology and ontology in the biomedical domain, both from a theoretical perspective (quality assurance, interoperability) and in their application to natural language processing, knowledge discovery and information integration 

Dr. Bodenreider is a Fellow of the American College of Medical Informatics. He received a MD degree from the University of Strasbourg, France in 1990 and a PhD in Medical Informatics from the University of Nancy, France in 1993. Before joining the National Library of Medicine in 1996, he was assistant professor for Biostatistics and Medical Informatics at the University of Nancy Medical School.

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