Logical and Semantic Modeling of Complex Biomolecular Networks

Abstract

Systems biology models aim to describe and understand the behaviour of a cell. This living organism is represented by a complex biomolecular network. In the literature, most researches focus only on modeling isolated parts of this network, such as the metabolic network or the gene regulatory network. However, to fully understand the behaviour of a cell we should model and analyze the biomolecular network as a whole.Towards this goal, we firstly present a formalization for describing the logical structure, function and behaviour of complex biomolecular networks. In addition, we propose a semantic approach based on four ontologies to provide a rich description for modeling a biomolecular network and its state changes. This approach contributes to propose to the biologist a platform where to simulate the state changes of biomolecular networks with the hope of steering their behaviours.