Issues in reasoning about interaction networks in cells: Necessity of event ordering knowledge

In this paper we discuss several representation issues that we came across while modelling molecular interactions in cells of living organisms. One of the issues was that the triggering of events inside cells, an important modelling component, are not necessarily immediate, leading to multiple evolution models in the absence of additional information. Second, often an action or a trigger at one level of granularity of representation can be elaborated and refined. We show the problem that existing representation and modelling formalisms have in dealing with the above issues. We then present an action language which builds up on a previous language, and has the ability to express event ordering knowledge. We show that our language is able to adequately address the above-mentioned issues.