An Algorithm for the Identification of Components in Biochemical Pathways

Biochemical pathways are abstract descriptions of the interactions among the molecular species involved in a process. Different molecular species mentioned in a pathway often represent different states of the same biological entity (e.g. the unbound and bound states of a certain molecule). Hence, a pathway can be seen as a network of interactions between entities which may change state synchronously by means of reactions. We consider such biological entities as pathway components and define a semi-automatic algorithm to infer the components from their interactions described in the pathway. Since this problem is inherently ambiguous, interaction with a domain expert might be needed to resolve any ambiguity that should arise. We apply the algorithm to the identification of components in a model of the EGF signaling pathway from the literature, and discuss possible uses of the component categorization as regards (i) the extraction of subpathways by projecting over a subset of components, and (ii) the automatic translation into finite state automata or process algebra terms.