The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways.
BACKGROUND
There is general agreement amongst biologists about the need for good pathway diagrams and a need to formalize the way biological pathways are depicted. However, implementing and agreeing how best to do this is currently the subject of some debate.


RESULTS
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.


CONCLUSIONS
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.
Freeman
Tom C
TC
Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK. Tom.Freeman@roslin.ed.ac.uk
Raza
Sobia
S
Theocharidis
Athanasios
A
Ghazal
Peter
P
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D006801:Humans; D007107:Immune System; D008285:Major Histocompatibility Complex / Q000235:genetics; D051379:Mice; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology; D014584:User-Computer Interface