6 votes

Systems Biology Graphical Notation: Process Diagram Level 1

Nicolas Le Novere¹, Stuart Moodie², Anatoly Sorokin³, Michael Hucka⁴, Falk Schreiber⁵, Emek Demir⁶, Huaiyu Mi⁷, Yukiko Matsuoka⁸, Katja Wegner⁹ & Hiroaki Kitano⁸

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1. EMBL-EBI
2. CSBE, University of Edinburgh
3. University of Edinburgh
4. California Institute of Technology
5. IPK Gatersleben & MLU Halle
6. MSKCC Computational Biology Center
7. SRI International
8. The Systems Biology Institute
9. University of Hertfordshire

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Document Type:

Manuscript

Date:

Received 22 September 2008 20:40 UTC; Posted 23 September 2008

Subjects:

Biotechnology, Bioinformatics

Tags:

• systems biology
• modeling
• pathway
• graph

Abstract:

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.

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License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Le Novere, Nicolas, Moodie, Stuart, Sorokin, Anatoly, Hucka, Michael, Schreiber, Falk, Demir, Emek, Mi, Huaiyu, Matsuoka, Yukiko, Wegner, Katja, and Kitano, Hiroaki. Systems Biology Graphical Notation: Process Diagram Level 1. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.2320.1> (2008)

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