The Systems Biology Graphical Notation

Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I. Aladjem, Sarala M. Wimalaratne, Frank T. Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji, Lu Li, Yukiko Matsuoka, Alice Villéger, Sarah E. Boyd, Laurence Calzone, Melanie Courtot & 19 others Ugur Dogrusoz, Tom C. Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B. Kell, Chris Sander, Herbert Sauro, Jacky L. Snoep, Kurt Kohn, Hiroaki Kitano

Research output: Contribution to journalArticle

480 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)735-741
Number of pages7
JournalNature Biotechnology
Volume27
Issue number8
DOIs
StatePublished - Aug 2009
Externally publishedYes

Fingerprint

Systems Biology
Visual languages
Language
Cell signaling
Unified Modeling Language
Metabolism
Gene expression
Visualization
Software
Networks (circuits)
Communication
Genes

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Biotechnology
  • Molecular Medicine
  • Bioengineering
  • Biomedical Engineering

Cite this

Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., ... Kitano, H. (2009). The Systems Biology Graphical Notation. Nature Biotechnology, 27(8), 735-741. https://doi.org/10.1038/nbt.1558

The Systems Biology Graphical Notation. / Novère, Nicolas Le; 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.

In: Nature Biotechnology, Vol. 27, No. 8, 08.2009, p. 735-741.

Research output: Contribution to journalArticle

Novère, NL, 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 2009, 'The Systems Biology Graphical Notation', Nature Biotechnology, vol. 27, no. 8, pp. 735-741. https://doi.org/10.1038/nbt.1558
Novère NL, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A et al. The Systems Biology Graphical Notation. Nature Biotechnology. 2009 Aug;27(8):735-741. https://doi.org/10.1038/nbt.1558
Novère, Nicolas Le ; 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. / The Systems Biology Graphical Notation. In: Nature Biotechnology. 2009 ; Vol. 27, No. 8. pp. 735-741.
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