In recent years there has been a steady growth in the number of papers describing results derived from molecular systems biology approaches (1). However, there is a need for a unified implementation of related languages and notations that can be read by both humans and computers (2,3).
An international team initiated by Dr Hiroaki Kitano (Systems Biology Institute, Japan) and coordinated by Dr Nicolas Le Novère (European Bioinformatics Institute, UK) has published a recent paper in Nature Biotechnology describing the Systems Biology Graphical Notation (SBGN) (1).
It consists of three complementary languages: Process Description ("Representing processes that convert physical entities into other entities, change their states or change their location"), Entity relationship ("Representing the interactions between entities and the rules that control them") and Activity flow ("Representing the influence of biological activities on each other").
Activity Flow diagrams are similar to the schemes used in papers describing results from functional genomics experiments. There are several freely available programs that are implementing SBGN.
A broad implementation of the SBGN will be useful to discover and describe in further detail pathways and networks underlying complex phenotypes and diseases (2,3,4).
Nicolas Le Novère, PhD
Group Leader, Computational Neurobiology Group
European Bioinformatics Institute, UK
(1) Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug;27(8):735-41. (Freely Available Full Text)
(2) Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature. 1999 Dec 2;402(6761 Suppl):C47-52.
(3) Lazebnik Y. Can a biologist fix a radio?--Or, what I learned while studying apoptosis. Cancer Cell. 2002 Sep;2(3):179-82.
(4) Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature. 2009 Sep 10;461(7261):218-23.
What is the biggest challenge for a broad implementation of the SBGN?
"The availability of easy to use software and toolkits. The community is now actively developing such software support." Nicolas Le Novère, PhD
Systems Biology Graphical Notation website
Diego Forero, MD
Message posted by: Diego Forero