The Systems Biology Graphical Notation

The Systems Biology Graphical Notation

VOLUME 27 NUMBER 8 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 Ghazal4,14, Hideya Kawai15, Lu Li1, Yukiko Matsuoka16, Alice Villéger17,18, Sarah E Boyd19, Laurence Calzone20, Melanie Courtois21, Ugur Dogruso22, 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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[slides and audio] The Systems Biology Graphical Notation