Standard Formats

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SBGN Process Description language Level 1 Version 1.3


PD describes each process in a network in great detail.


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, specialized 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.*

*(Moodie, Stuart  et al.. Available from Nature Precedings (2011))

Publication Date



Moodie, Stuart
Le Novère, Nicolas
Mi, Huaiyu
Demir, Emek
Schreiber, Falk


Biological Scales

Scale molecular cellular tissue organ organism ecosystem
Support intrinsic unknown unknown unknown unknown unknown

Spatial Representation

Spatial Representation Level Compartment Dimensions Gradients Spatial Structures
Support intrinsic unknown unknown unknown

Modeling Formalisms for this format

Software support for this format

Examples for this format


  • Standardized graphical layout of a model

Modularity: no

Components Relation
Flat Network: no

Supported Math

Unit Support

Unit Required: no

Support: no support

Annotation Support

Miriram Support: no Support: no


Additional information on glyphs uses controlled vocabulary from SBO.


Programming language





Systems Biology Graphical Notation (SBGN)


Systems Biology Graphical Notation aims at representing networks of biochemical interactions in a standard and unambigious way.

Publication date






All formats for this class

Free and Open


Not closely defiened license allowing for free use and open participation. The product is viewed as community effort.