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Open Access Research article

The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways

Tom C Freeman12*, Sobia Raza12, Athanasios Theocharidis12 and Peter Ghazal13

Author Affiliations

1 Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK

2 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK

3 Centre for Systems Biology at Edinburgh, C H Waddington Building, King's Buildings, Mayfield Road, Edinburgh, EH9 3JU, UK

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BMC Systems Biology 2010, 4:65  doi:10.1186/1752-0509-4-65

Published: 17 May 2010

Abstract

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.