Formal modeling of approximate relations in biochemical systems

Abstract

Aiming to satisfy the need for the formalization of semiquantitative reasoning in the analysis of biochemical systems, the O[M] formalism for reasoning with orders of magnitude and approximate relations has been developed. It is based on seven primitive relations among quantities and compound relations which are formed as implicit disjunctions of primitives. O[M] can perform inferences by using formal approximate relations, algebraic equations, inequalities, if-then rules, assumptions, and goals. The applications discussed include Michaelis-Menten kinetics, different modes of inhibition of an enzymatic reaction, analysis of fluxes in biochemical networks, and identification of rate-limiting steps of biochemical pathways. In these applications, O[M] provides a medium for acquisition and formalization of previously informal concepts, analysis of systems at the order-of-magnitude level of detail, and automation of commonsense reasoning.