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A Graphical Notation to describe the Logical Interactions of Biological Pathways

Moodie, Stuart L. ; Sorokin, Anatoly ; Goryanin, Igor ; Ghazal, Peter

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
The modelling of biological intra-cellular pathways requires the systematic capture and representation of interactions between components that are biologically correct and computationally rigorous. The challenge is two fold, to verify and extend our understanding of such pathways by comparing in silico models to experiments; and to ensure that such models are understandable by biologists and for checking biological validity. In this report we present a graphical notation, the Edinburgh Pathway Notation (EPN), which satisfies the central biologically driven requirements while providing a strict formal framework for analysis. The EPN emphasises the use of a logical representation of pathways, which is particularly suited to pathways were some mechanisms are not known in detail.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Moodie, Stuart L. ; Sorokin, Anatoly ; Goryanin, Igor ; Ghazal, Peter  (2006)  A Graphical Notation to describe the Logical Interactions of Biological Pathways. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 3(2), 2006. Special Issue: 3rd Integrative Bioinformatics Workshop, Harpenden, United Kingdom, 2

Online-Journal: http://journal.imbio.de/index.php?paper_id=36
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2007/217

Also published by Shaker:
Ralf Hofestädt, Thoralf Töpel (eds.). Integrative Bioinformatics -
Yearbook 2006. Shaker, 2007.


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