This chapter proposes a new logical model based on a fragment of the first-order logic capable of describing reactions that appear in a metabolic network. It presents an efficient automated deduction method that can answer queries by deduction to predict reaction results or by abductive reasoning to find reactions and protein states. This automated deduction method is based on a translation procedure that transforms the first-order formulas into quantifier-free formulas. The goal of the chapter is to design and develop software that allows the interactive visualization of molecular interaction maps (MIMs). The chapter also presents a basic language capable of modeling some basic positive and negative interactions between two or more proteins in a pathway. It focuses on the activation and inhibition actions, and then shows how this language can be extended to express the different other actions, as the action of phosphorylation, autophosphorylation and binding.