Central to a coherent understanding of cellular biology is a faithful representation of biochemical processes as it pertains to its molecular participants. Current representations underspecify our knowledge because they fail to indicate the roles of the molecular components during relevant processes. Here, we describe a knowledge representation using OWL2 that overcomes previous limitations in modeling biochemical events and has clear implications for the accurate functional/role based annotation of molecular components. paper: http://dumontierlab.com/pdf/2008_OWLEDEU_MR.pdf

1. Situational Modeling: Defining Molecular Roles in Biochemical Pathways and Reactions Michel Dumontier , PhD Assistant Professor of Bioinformatics Department of Biology, School of Computer Science, Institute of Biochemistry, Ottawa Institute of Systems Biology Carleton University

6. Ontology

8. Roles for all the important parts Mechanistic Event Decomposition