TY - JOUR
T1 - The Systems Biology Graphical Notation
AU - Novère, Nicolas Le
AU - Hucka, Michael
AU - Mi, Huaiyu
AU - Moodie, Stuart
AU - Schreiber, Falk
AU - Sorokin, Anatoly
AU - Demir, Emek
AU - Wegner, Katja
AU - Aladjem, Mirit I.
AU - Wimalaratne, Sarala M.
AU - Bergman, Frank T.
AU - Gauges, Ralph
AU - Ghazal, Peter
AU - Kawaji, Hideya
AU - Li, Lu
AU - Matsuoka, Yukiko
AU - Villéger, Alice
AU - Boyd, Sarah E.
AU - Calzone, Laurence
AU - Courtot, Melanie
AU - Dogrusoz, Ugur
AU - Freeman, Tom C.
AU - Funahashi, Akira
AU - Ghosh, Samik
AU - Jouraku, Akiya
AU - Kim, Sohyoung
AU - Kolpakov, Fedor
AU - Luna, Augustin
AU - Sahle, Sven
AU - Schmidt, Esther
AU - Watterson, Steven
AU - Wu, Guanming
AU - Goryanin, Igor
AU - Kell, Douglas B.
AU - Sander, Chris
AU - Sauro, Herbert
AU - Snoep, Jacky L.
AU - Kohn, Kurt
AU - Kitano, Hiroaki
N1 - Funding Information:
In the version of this article initially published, the following acknowledgment was inadvertently left out: “The UCSF CPTAC team gratefully acknowledges the support of the Canary Foundation for providing funds to purchase a 4000 QTRAP mass spectrometer.” The acknowlegment has been added to the HTML and PDF versions of the article.
Funding Information:
The development of SBGN was mainly supported by a grant from the New Energy and Industrial Technology Development Organization of the Japanese government. SBGN workshops also benefited from funding by the following organizations: the UK Biotechnology and Biological Sciences Research Council, the National Institute of Advanced Industrial Science and Technology of Japan, the Okinawa Institute of Science and Technology), the European Media Laboratory, Heidelberg, Germany and the Beckman Institute at the California Institute of Technology, Pasadena, California, USA. Attendance at the meetings by Japanese authors was supported by the Japan Science and Technology Agency and by the genome network project of the Japanese Ministry of Education, Culture, Sports, Science, and Technology. I.G., S.M. and A.S. acknowledge support by the British Engineering and Physical Sciences Research Council. F.T.B. acknowledges support by the National Institutes of Health (NIH; grant 1R01GM081070-01). The contributions of M.I.A., S.K., A.L. and K.K. were supported by the Intramural Research Program of the NIH, Center for Cancer Research, National Cancer Institute (NIH).
PY - 2009/8
Y1 - 2009/8
N2 - 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.
AB - 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.
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U2 - 10.1038/nbt.1558
DO - 10.1038/nbt.1558
M3 - Review article
C2 - 19668183
AN - SCOPUS:68449103579
SN - 1087-0156
VL - 27
SP - 735
EP - 741
JO - Nature Biotechnology
JF - Nature Biotechnology
IS - 8
ER -