PD2AF converter is an open-source application designed to enable communication between the Process Description (PD) and the Activity Flow (AF) languages of the Systems Biology Graphical Notation (SBGN) standard. The purpose of the tool is to translate PD to AF in such a way so it produces the result comparable to manually designed AF diagrams and the corresponding logical models.

Translation rule highlight

Activation of protein phosphorylation: active unphosphorylated state

Associated GO term: GO:0001934 positive regulation of protein phosphorylation


SBGN-MLNewt

SBGN-MLNewt

This is a case of a "hidden" inhibition: from the Process Description version it is not obvious that this is an inhibition because the mechanism is shown in details and the inhibition arc is not used. Protein A stimulates a process of protein B deactivation (the state of the left is shown as active), and therefore in Activity Flow it is represented by the protein A activity inhibiting the protein B activity.