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 visual language developed by a community of biochemists, modelers, and computer scientists to standardize the representation of biochemical interactions. Unlike existing graphical notations, SBGN consists of three complementary languages: process diagrams, entity relationship diagrams, and activity flow diagrams. These enable scientists to represent biochemical networks in a standard, unambiguous way, facilitating efficient and accurate representation, visualization, storage, exchange, and reuse of biological knowledge.
SBGN was developed in response to the lack of standard graphical notations in biology, despite the visual nature of much biological information. Previous efforts lacked standardization, leading to ambiguity and inconsistency. SBGN aims to address these issues by providing a systematic and unambiguous graphical notation. It is designed to be free of intellectual property restrictions, syntactically and semantically consistent, and to support the representation of diverse biological objects and their interactions.
SBGN is structured into three orthogonal diagram types: process diagrams, entity relationship diagrams, and activity flow diagrams. Process diagrams depict molecular processes and interactions, entity relationship diagrams focus on the influences between entities, and activity flow diagrams show the cascade of activities. Each diagram type has its own strengths and is used to represent different aspects of biological systems.
SBGN is designed to be modular, visually consistent, and to support automated diagram generation from mathematical models. It avoids the combinatorial explosion of possible entities and reactions by focusing on essential elements. The notation is also designed to be easily understandable, with a minimal number of symbols and syntax.
SBGN is intended to be used by a diverse community of biologists, biochemists, bioinformaticians, geneticists, theoreticians, and software engineers. The development of SBGN is guided by principles that ensure its usability, clarity, and adaptability. The notation is expected to facilitate the exchange and reuse of biological knowledge, supporting research in molecular, systems, and synthetic biology.The Systems Biology Graphical Notation (SBGN) is a visual language developed by a community of biochemists, modelers, and computer scientists to standardize the representation of biochemical interactions. Unlike existing graphical notations, SBGN consists of three complementary languages: process diagrams, entity relationship diagrams, and activity flow diagrams. These enable scientists to represent biochemical networks in a standard, unambiguous way, facilitating efficient and accurate representation, visualization, storage, exchange, and reuse of biological knowledge.
SBGN was developed in response to the lack of standard graphical notations in biology, despite the visual nature of much biological information. Previous efforts lacked standardization, leading to ambiguity and inconsistency. SBGN aims to address these issues by providing a systematic and unambiguous graphical notation. It is designed to be free of intellectual property restrictions, syntactically and semantically consistent, and to support the representation of diverse biological objects and their interactions.
SBGN is structured into three orthogonal diagram types: process diagrams, entity relationship diagrams, and activity flow diagrams. Process diagrams depict molecular processes and interactions, entity relationship diagrams focus on the influences between entities, and activity flow diagrams show the cascade of activities. Each diagram type has its own strengths and is used to represent different aspects of biological systems.
SBGN is designed to be modular, visually consistent, and to support automated diagram generation from mathematical models. It avoids the combinatorial explosion of possible entities and reactions by focusing on essential elements. The notation is also designed to be easily understandable, with a minimal number of symbols and syntax.
SBGN is intended to be used by a diverse community of biologists, biochemists, bioinformaticians, geneticists, theoreticians, and software engineers. The development of SBGN is guided by principles that ensure its usability, clarity, and adaptability. The notation is expected to facilitate the exchange and reuse of biological knowledge, supporting research in molecular, systems, and synthetic biology.