Sunday, May 11, 2014

Systems Biology Graphical Notation

I have been reading the pertinent literature in regards to two portions of the Systems Biology Graphical Notation specifications:

1. Process Description Language
2. Activity Flow Language

Let us discuss each in turn.

According to the SBGN website, the "Process Description language 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".

Reference Card for SBGN symbols
Let us examine an example process description map(from page 57 of the specifications PDF) using the above reference card.

Onto the Activity Flow language specification:

The Activity Flow Language "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".

An Activity Flow Description map is annotated below.

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