The Systems Biology Graphical Notation

The Systems Biology Graphical Notation

August 2009 | Nicolas Le Novère¹, Michael Hucka², Huaiyu Mi³, Stuart Moodie⁴, Falk Schreiber⁵,⁶, Anatoly Sorokin⁷, Emek Demir⁸, Katja Wegner⁹, Mirit I Aladjem¹⁰, Sarala M Wimalaratne¹¹, Frank T Bergman¹², Ralph Gauges¹³, Peter Ghazal¹⁴,¹⁵, Hideya Kawaji¹⁵, Lu Li¹, Yukiko Matsuoka¹⁶, Alice Villéger¹⁷,¹⁸, Sarah E Boyd¹⁹, Laurence Calzone²⁰, Melanie Courtot²¹, Ugur Dogrusoz²², Tom C Freeman¹⁴,²³, Akira Funahashi²⁴, Samik Ghosh¹⁶, Akiya Jouraku²⁴, Sohyoung Kim¹⁰, Fedor Kolpakov²⁵,²⁶, Augustin Luna¹⁰, Sven Sahle¹³, Esther Schmidt¹, Steven Watterson⁴,²², Guanming Wu²⁷, Igor Goryanin⁴, Douglas B Kell¹⁸,²⁸, Chris Sander⁸, Herbert Sauro¹², Jacky L Snoep²⁹, Kurt Kohn¹⁰ & Hiroaki Kitano¹⁶,³⁰,³¹
The Systems Biology Graphical Notation (SBGN) is a community-developed visual language designed to standardize the representation of biochemical interaction networks. SBGN consists of three complementary languages: process diagrams, entity relationship diagrams, and activity flow diagrams. These languages enable scientists to represent complex biological networks in a standardized and unambiguous manner, facilitating efficient communication, visualization, storage, exchange, and reuse of biological knowledge. The development of SBGN was driven by the need to address the lack of standard graphical notations in biology, which has hindered the sharing and integration of diverse biological data. SBGN aims to specify the connectivity of graphs and the types of nodes and edges, without specifying their precise layout or colors. The notation is designed to be manageable and evolve in stages, with each higher level adding more complexity while maintaining compatibility with lower levels. The article also discusses the historical antecedents of graphical notations in biology and the challenges faced in developing a comprehensive and widely accepted standard. The SBGN project has involved a community-based approach, involving multiple groups and individuals, to ensure its success and relevance in the field of systems biology.The Systems Biology Graphical Notation (SBGN) is a community-developed visual language designed to standardize the representation of biochemical interaction networks. SBGN consists of three complementary languages: process diagrams, entity relationship diagrams, and activity flow diagrams. These languages enable scientists to represent complex biological networks in a standardized and unambiguous manner, facilitating efficient communication, visualization, storage, exchange, and reuse of biological knowledge. The development of SBGN was driven by the need to address the lack of standard graphical notations in biology, which has hindered the sharing and integration of diverse biological data. SBGN aims to specify the connectivity of graphs and the types of nodes and edges, without specifying their precise layout or colors. The notation is designed to be manageable and evolve in stages, with each higher level adding more complexity while maintaining compatibility with lower levels. The article also discusses the historical antecedents of graphical notations in biology and the challenges faced in developing a comprehensive and widely accepted standard. The SBGN project has involved a community-based approach, involving multiple groups and individuals, to ensure its success and relevance in the field of systems biology.
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