The Systems Biology Graphical Notation

Creators: Le Novère, Nicolas; Hucka, Michael; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Sorokin, Anatoly; Demir, Emek; Wegner, Katja; Aladjem, Mirit I.; Wimalaratne, Sarala M.; Bergman, Frank T.; Gauges, Ralph; Ghazal, Peter; Kawaji, Hideya; Li, Lu; Matsuoka, Yukiko; Villéger, Alice; Boyd, Sarah E.; Calzone, Laurence; Courtot, Melanie; Dogrusoz, Ugur; Freeman, Tom C.; Funahashi, Akira; Ghosh, Samik; Jouraku, Akiya; Kim, Sohyoung; Kolpakov, Fedor; Luna, Augustin; Sahle, Sven; Schmidt, Esther; Watterson, Steven; Wu, Guanming; Goryanin, Igor; Kell, Douglas B.; Sander, Chris; Sauro, Herbert; Snoep, Jacky L.; Kohn, Kurt; Kitano, Hiroaki

Abstract

Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.

Additional Information

© 2009 Nature Publishing Group. Published online: 7 August 2009. Corrected online: 9 September 2009. There is an Erratum (September 2009) associated with this Perspective. The development of SBGN was mainly supported by a grant from the New Energy and Industrial Technology Development Organization of the Japanese government. SBGN workshops also benefited from funding by the following organizations: the UK Biotechnology and Biological Sciences Research Council, the National Institute of Advanced Industrial Science and Technology of Japan, the Okinawa Institute of Science and Technology), the European Media Laboratory, Heidelberg, Germany and the Beckman Institute at the California Institute of Technology, Pasadena, California, USA. Attendance at the meetings by Japanese authors was supported by the Japan Science and Technology Agency and by the genome network project of the Japanese Ministry of Education, Culture, Sports, Science, and Technology. I.G., S.M. and A.S. acknowledge support by the British Engineering and Physical Sciences Research Council. F.T.B. acknowledges support by the National Institutes of Health (NIH; grant 1R01GM081070-01). The contributions of M.I.A., S.K., A.L. and K.K. were supported by the Intramural Research Program of the NIH, Center for Cancer Research, National Cancer Institute (NIH). Note: Supplementary information is available on the Nature Biotechnology website. The authors declare competing financial interests.

Errata

Nat. Biotechnol. 27735–741 (2009); published online 7 August 2009; corrected after print 11 August 2009 In the version of this article initially published, the wrong versions of Figures 1, 2 and 3 were used. The error has been corrected in the HTML and PDF versions of the article. http://www.nature.com/uidfinder/10.1038/nbt0909-864d

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