Figure 8. The principles of conversion to the edge-labelled graph format.

A) Activation reaction (labelled A) reaction between two components is transformed into the graph with arcs between the reactant and the product node. B) Activation (labelled A) on a transcription level is a special type of activation, when Y induces the activation of gene X to produce protein X. In this case we omit the gene transcription level when transforming the level 2 topology to the edge-labelled graph. C) Binding (labelled B) relation between two reactant nodes X and Y is transformed into a B relation between the reactants and an additional relation produces (labelled as P) between the reactant and the product. The latter is introduced to represent the binding of proteins into complexes. Binding is a binary relation, consisting of a bidirectional edge; in graph visualisation, the arrows are omitted. D) Inhibition (labelled I) is the blocking of the activation or binding reaction between components by a third component X, resulting in reduced production of product Z.