Understanding the Behaviour of Complex Biomolecular Networks by Combining Logical and Semantic Modeling

In literature, most researches related to the understanding of the behaviour of the cell networks focus only on some parts of the biomolecular network. However, to completely understand their behaviour over time we have to integrate the different parts of the biomolecular network and analyse them together. The objective of the present study is to propose to the biologist a platform to simulate the state changes of biomolecular networks with the hope of steering their behaviours. In this paper, we firstly present an efficient formalism to represent the dynamic behaviour of biomolecular networks. This logical model is based on the three levels of systems theory: structural, functional and behavioural modeling. We then propose a semantic approach based on four ontologies to formalise the domain knowledge of complex biomolecular networks. Both of these approaches provide the necessary elements to model, analyse and understand the dynamic behaviour and the transition states of these networks.