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[protege-discussion] NCBO Webinar: Michel Dumontier, Feb. 15 - Formalization of models and simulation results in systems biology

Trish Whetzel plwhetzel at
Fri Feb 10 14:35:04 PST 2012

The next NCBO Webinar will be presented by Michel Dumontier from Carleton
University on "Formalization of models and simulation results in systems
biology" at 10:00am PT, Wednesday, February 15.  Below is information on
how to join the online meeting via WebEx and accompanying teleconference.
For the full schedule of the NCBO Webinar presentations see:

Computational systems biology provides insight into the dynamics of
biological systems through computable models based on high quality data. As
models get more and more sophisticated, we need to be able to assess their
accuracy against current knowledge as well as expected behaviour. In this
talk, I will discuss our efforts to formalize SBML model annotations and
link them to biological entities typically described in biomedical
ontologies. Using the SBML Harvester, we generated a large knowledge base
from the BioModels Database and demonstrate sophisticated biological
queries involving different types of molecules, their functions and their
locations in cellular and anatomical structures. Through automated
reasoning, we uncovered errors arising both from SBML abuse and from manual
curation. We further formalized time-course simulations and their results,
so as to provide insight into molecular and cellular behaviour.  Our work
marks a first step towards establishing a bi-directional information flow
between systems biology and biomedical ontologies, towards supporting
large-scale analyses of biological systems with an integrated systems
biology framework for biological knowledge discovery.

Dr. Michel Dumontier is an Associate Professor of Bioinformatics in the
Department of Biology, the Institute of Biochemistry and School of Computer
Science at Carleton University in Ottawa, Canada. His research aims to
develop semantics-powered computational methods to increase our
understanding of how living systems respond to chemical agents. At the core
of the research program is the development and use of Semantic Web
technologies to formally represent and reason about data and services so as
(1) to facilitate the publishing, sharing and discovery of scientific
knowledge produced by individuals and small collectives, (2) to enable the
formulation and evaluation scientific hypotheses using our collective tools
and knowledge and (3) to create and make available computational methods to
investigate the structure, function and behaviour of living systems. Dr.
Dumontier currently serves as a chair for the World Wide Web Consortium
Semantic Web in Health Care and Life Sciences Interest Group (W3C HCLSIG),
and is currently on sabbatical at Stanford University.

To start or join the online meeting
Go to
Meeting Password: ncbo

Audio conference information
To receive a call back, provide your phone number when you join the
meeting, or call the number below and enter the access code.
Call-in toll number (US/Canada): 1-650-429-3300
Global call-in numbers:

Access code:925 756 393

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378

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