Component identification in biochemical pathways

Abstract

Biochemical pathways are abstract descriptions of the interactions among the molecular species involved in a cellular process. Different molecular species mentioned in a pathway often represent different states of the same biological entity, such as the unbound and bound states of a certain molecule. Hence, a pathway can be seen as a network of interactions between entities changing state synchronously by means of reactions. We consider such biological entities as pathway components.We define a semi-automatic algorithm to infer the components from their interactions described in the pathway. In case the interactions are not sufficient to resolve all the reactions, help from a domain expert may be needed to resolve any ambiguity that should arise. As an example of application, we apply the algorithm to a model of the EGF signaling pathway from the literature in order to identify its components. From the theoretical point of view, we formally prove the correctness of the algorithm, its termination under any input pathway and a (weak) confluence property.