The Systems Biology Graphical Notation

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

    Research output: Contribution to journalArticle

    475 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.
    LanguageEnglish
    Pages735-741
    JournalNature Biotechnology
    Volume27
    DOIs
    Publication statusPublished - 7 Aug 2009

    Fingerprint

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

    Keywords

    • SBGN
    • Graphical Notation
    • Cartoon
    • Diagram

    Cite this

    Novere, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., ... Kitano, H. (2009). The Systems Biology Graphical Notation. Nature Biotechnology, 27, 735-741. https://doi.org/10.1038/nbt.1558
    Novere, Nicolas Le ; Hucka, Michael ; Mi, Huaiyu ; Moodie, Stuart ; Schreiber, Falk ; Sorokin, Anatoly ; Demir, Emek ; Wegner, Katja ; Aladjem, Mirit ; Wimalaratne, Sarala ; Bergman, Frank ; Gauges, Ralph ; Ghazal, Peter ; Kawaji, Hideya ; Li, Lu ; Matsuoka, Yukiko ; Villeger, Alice ; Boyd, Sarah ; Calzone, Laurence ; Courtot, Melanie ; Dogrusoz, Ugur ; Freeman, Tom ; Funahashi, Akira ; Ghosh, Samik ; Jouraku, Akiya ; Kim, Sohyoung ; Kolpakov, Fedor ; Luna, Augustin ; Sahle, Sven ; Schmidt, Esther ; Watterson, Steven ; Wu, Guanming ; Goryanin, Igor ; Kell, Douglas ; Sander, Chris ; Sauro, Herbert ; Snoep, Jacky ; Kohn, Kurt ; Kitano, Hiroaki. / The Systems Biology Graphical Notation. In: Nature Biotechnology. 2009 ; Vol. 27. pp. 735-741.
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    Novere, NL, Hucka, M, Mi, H, Moodie, S, Schreiber, F, Sorokin, A, Demir, E, Wegner, K, Aladjem, M, Wimalaratne, S, Bergman, F, Gauges, R, Ghazal, P, Kawaji, H, Li, L, Matsuoka, Y, Villeger, A, Boyd, S, Calzone, L, Courtot, M, Dogrusoz, U, Freeman, T, Funahashi, A, Ghosh, S, Jouraku, A, Kim, S, Kolpakov, F, Luna, A, Sahle, S, Schmidt, E, Watterson, S, Wu, G, Goryanin, I, Kell, D, Sander, C, Sauro, H, Snoep, J, Kohn, K & Kitano, H 2009, 'The Systems Biology Graphical Notation', Nature Biotechnology, vol. 27, pp. 735-741. https://doi.org/10.1038/nbt.1558

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

    In: Nature Biotechnology, Vol. 27, 07.08.2009, p. 735-741.

    Research output: Contribution to journalArticle

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    Novere NL, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A et al. The Systems Biology Graphical Notation. Nature Biotechnology. 2009 Aug 7;27:735-741. https://doi.org/10.1038/nbt.1558