Here's the revised section:




Diagrams are used extensively in a variety of ways in biology, and this project is an attempt to clarify and standardize their different uses:

* [Systems Biology Graphical Notation (SBGN)](http://www.sbgn.org/Main_Page) homepage.

SBGN is made up of three different languages, representing different visions of biological systems. Each language involves a comprehensive set of symbols with precise semantics, together with detailed syntactic rules how maps are to be interpreted:

* The SBGN [Process Description (PD) language](http://precedings.nature.com/documents/3721/version/2) shows the temporal courses of biochemical interactions in a network. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram. Process Descriptions correspond to systems of ordinary differential equations.

PD

* The SBGN [Entity Relationship (ER) language](http://precedings.nature.com/documents/3719/version/2) allows you to see all the relationships in which a given entity participates, regardless of the temporal aspects. Relationships can be seen as rules describing the influences of entities nodes on other relationships. Entity Relationships correspond to rule-based models (e.g. models encoded in [[BioNetGen]], [[Kappa]], etc.).

ER

* The SBGN [Activity Flow (AF) language](http://precedings.nature.com/documents/3724/version/1) depicts the flow of information between biochemical entities in a network. It omits information about the state transitions of entities and is particularly convenient for representing the effects of perturbations, whether genetic or environmental in nature. Activity Flows correspond to logical models of the sort used by Stuart Kauffman and Rene Thomas.

AF