Formalization of models and simulation results in systems biology


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.