The Systems Biology Graphical Notation Journal Article
| Authors: | Novère, N. L.; Hucka, M.; Mi, H.; Moodie, S.; Schreiber, F.; Sorokin, A.; Demir, E.; Wegner, K.; Aladjem, M. I.; Wimalaratne, S. M.; Bergman, F. T.; Gauges, R.; Ghazal, P.; Kawaji, H.; Li, L.; Matsuoka, Y.; Villéger, A.; Boyd, S. E.; Calzone, L.; Courtot, M.; Dogrusoz, U.; Freeman, T. C.; Funahashi, A.; Ghosh, S.; Jouraku, A.; Kim, S.; Kolpakov, F.; Luna, A.; Sahle, S.; Schmidt, E.; Watterson, S.; Wu, G.; Goryanin, I.; Kell, D. B.; Sander, C.; Sauro, H.; Snoep, J. L.; Kohn, K.; Kitano, H. |
| Article Title: | The Systems Biology Graphical Notation |
| 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. © 2009 Nature America, Inc. |
| Keywords: | signal transduction; review; accuracy; biology; internet; information processing; history, 20th century; gene control; molecular biology; language; computer program; computer graphics; software; gene regulations; activity flow; biochemical interactions; cellular signaling; circuit diagrams; complex information; computer scientists; entity relationship diagrams; graphical notation; process diagram; software tool; systems biology; textual information; unified modeling language diagrams; visual language; knowledge representation; linguistics; query languages; standards; unified modeling language; metabolic regulation |
| Journal Title: | Nature Biotechnology |
| Volume: | 27 |
| Issue: | 8 |
| ISSN: | 1087-0156 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2009-08-01 |
| Start Page: | 735 |
| End Page: | 741 |
| Language: | English |
| DOI: | 10.1038/nbt.1558 |
| PUBMED: | 19668183 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 42" - "Export Date: 30 November 2010" - "CODEN: NABIF" - "Source: Scopus" |
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