%0 Journal Article
%T The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways
%A Tom C Freeman
%A Sobia Raza
%A Athanasios Theocharidis
%A Peter Ghazal
%J BMC Systems Biology
%D 2010
%I BioMed Central
%R 10.1186/1752-0509-4-65
%X The modified Edinburgh Pathway Notation (mEPN) scheme is founded on a notation system originally devised a number of years ago and through use has now been refined extensively. This process 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 signaling in mammals. Here we provide a specification of the mEPN notation, its symbols, rules for its use and a comparison to the proposed Systems Biology Graphical Notation (SBGN) scheme.We hope this work will contribute to the on-going community effort to develop a standard for depicting pathways and will provide a coherent guide to those planning to construct pathway diagrams of their biological systems of interest.Pathway diagrams are currently available in a plethora of different forms. Using the term in the broadest sense, they can be a picture that accompanies a review article, wall charts distributed by journals and companies, small schematic diagrams used to support mathematical modeling efforts or network graphs reflecting known protein interactions based on the results of large scale interaction studies or automated literature mining. To support these efforts there are also a growing number of databases that serve up these 'pathways' [1]. These are either curated centrally [2-5] or increasingly by the community [6-8]. The sheer range of resources available reflects the current interest in pathway science. However, this variety can in itself be frustrating. Pathways are drawn using informal and idiosyncratic notation systems, with varying degrees of accuracy and specificity in defining what pathway components are being depicted and the relationships between them. Resources are often fragmented with some proteins or metabolites being members of numerous pathways; the concept of pathway membership being a highly subjective division. The pathways themselves are rarely available as a cohesive network and there are nu
%U http://www.biomedcentral.com/1752-0509/4/65