New Meetup: Increasingly Accurate Representation of Biochemistry

From: Melanie C.
Sent on: Sunday, April 26, 2009 2:03 PM
Announcing a new Meetup for The Vancouver Semantic Web Meetup Group!

What: Increasingly Accurate Representation of Biochemistry

When: May 21,[masked]:00 PM

Where: Click the link below to find out!

Meetup Description: Dr. Michel Dumontier will be visiting Vancouver before the Canadian Semantic Web Working Symposium ( and offered to present part of his work to our group. More details below.

Biochemical ontologies aim to capture and represent biochemical entities and the relations that exist between them in an accurate manner. A fundamental starting point is biochemical identity, but our current approach for generating identifiers is haphazard and consequently integrating data is error-prone. I will discuss plausible structure-based strategies for biochemical identity whether it be at molecular level or some part thereof (e.g. residues, collection of residues, atoms, collection of atoms, functional groups) such that identifiers may be generated in an automatic and curator/database independent manner. With structure-based identifiers in hand, we will be in a position to more accurately capture context-specific biochemical knowledge, such as how a set of residues in a binding site are involved in a chemical reaction including the fact that a key nitrogen atom must first be de-protonated. Thus, our current representation of biochemical knowledge may improve such that manual and automatic methods of bio-curation are substantially more accurate.

Dr. Michel Dumontier is an Assistant Professor of Bioinformatics at Carleton University. His research aims to develop a computational platform for personalized medicine. With over 35 research publications in workshops, conferences, and journals, his innovative research program is developing exciting opportunities to facilitate pharmacogenomic based knowledge discovery through improved knowledge representation, data
integration, molecular modeling and simulation. His appointments in the Department of Biology, Institute of Biochemistry and School of Computer Science, the Ottawa Institute of Systems Biology and the Ottawa-Carleton Institute for Biomedical Engineering demonstrate the interdisciplinary nature of his research program.
Dr. Dumontier is active in developing and promoting new technologies for improved knowledge representation. He is a sponsored member of the World Wide Web (W3C) Working Group on the Web Ontology Language (OWL) and an invited expert for the W3C's Semantic Web in Health Care and Life Sciences Interest Group (HCLSIG). He has co-organized an international workshop on the Semantic Web in the Health Care and Life Sciences, as part of the HCLSIG outreach effort. Dr. Dumontier was recently an invited panelist on "An OWL2 Far?" at the 2008 International Semantic Web Conference (ISWC), the premier conference for work on the Semantic Web, and further participated a panelist on the challenges and opportunities OWL at the OWL Experiences and Design workshop (OWLED), for which he was subsequently elected as a member of steering committee.

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