Assembly of Logic-Based Diagrams of Biological Pathways

Abstract

The networks of molecular interactions that underpin cellular function are highly complex and dynamic. The topology, behaviour and logic of these systems, even on a relatively small scale, are far too complicated to understand intuitively. Furthermore, enormous amounts of systems-level data pertaining to the nature of genes and proteins, and their potential cellular interactions, have now been generated, but we struggle to interpret these data. There is therefore general agreement amongst biologists about the need for good pathway diagrams. However, the challenge of creating models that reflect our current understanding of these systems and displaying this information in an intuitive and logical manner is not trivial. The modified Edinburgh pathway notation (mEPN) scheme is founded on a notation system originally devised a number of years ago, but through use has now been refined extensively. This has been primarily driven by the author’s attempts to produce process diagrams for a diverse range of biological pathways, particularly with respect to immune signalling in mammals. Whilst requiring a considerable effort, the assembly of pathway models provides a resource for training, literature/data interpretation, computational pathway modelling and hypothesis generation. Here I discuss the mEPN scheme, its symbols and rules for its use and thereby hope to provide a coherent guide to those planning to construct pathway diagrams of their biological systems of interest.