A Taxonomy of Causality-Based Biological Properties

TL;DR

This paper introduces a formal taxonomy of causality-based properties in metabolic networks, providing a theoretical framework and verification method that abstract away from quantitative details to analyze metabolite production.

Contribution

It presents a novel formal characterization of causality properties in metabolic networks and a verification approach using an abstract semantics based on Chemical Ground Form calculus.

Findings

Successful application to a real metabolic pathway segment

Provides a new formal framework for causality in biological systems

Offers an effective method for property verification

Abstract

We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a theoretical point of view, biochemical reactions are abstractly represented as causal implications and the produced metabolites as causal consequences of the implication representing the corresponding reaction. The fact that a reactant is produced is represented by means of the chain of reactions that have made it exist. Such representation abstracts away from quantities, stoichiometric and thermodynamic parameters and constitutes the basis for the characterization of our properties. Moreover, we propose an effective method for verifying our properties based on an abstract model of system dynamics. This consists of a new abstract semantics for the system seen as a concurrent network and expressed using the Chemical Ground Form calculus. We illustrate an application of this framework to a portion of a real metabolic pathway.