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BMC Syst Biol. 2010 May 17;4:65. doi: 10.1186/1752-0509-4-65.

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

Author information

  • 1Division 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

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.

PMID:
20478018
[PubMed - indexed for MEDLINE]
PMCID:
PMC2878301
Free PMC Article

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