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Published September 23, 2008 | public
Journal Article

Systems Biology Graphical Notation: Process Diagram Level 1


Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.

Additional Information

© 2008 Nature Publishing Group. Received 22 September 2008 20:40 UTC; Posted 23 September 2008. The authors are grateful to all the attendees of the SBGN meetings, as well as to the subscribers of the sbgn-discuss@sbgn.org mailing list. The authors would like to acknowledge especially the help of Frank Bergmann, Sarala Dissanayake, Ralph Gauges, Peter Ghazal, and Lu Li. SM and AS would also like to acknowledge Igor Goryanin whose financial support and encouragement enabled us to commit the necessary time to the development of this specification. A more comprehensive list of people involved in SBGN development is available in the appendix D. The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO, http://www.nedo.go.jp/). The Okinawa Institute of Science and Technology (OIST, http://www.oist.jp/), the AIST Computational Biology Research Center (AIST CBRC, http://www.cbrc.jp/index.eng.html) the British Biotechnology and Biological Sciences Research Council (BBSRC, http://www. bbsrc.ac.uk/) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, http://www.eml-r.org/), and the Beckman Institute at the California Institute of Technology (http://bnmc.caltech.edu) provided additional support for SBGN workshops. Some help was provided by the Japan Science and Technology Agency (JST, http: //www.jst.go.jp/) and the Genome Network Project of the Japanese Ministry of Education, Sports, Culture, Science, and Technology (MEXT, http://www.mext.go.jp/) for the development of the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EPSRC, http://www.epsrc.ac.uk) during the redaction of the specification.

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