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The PD2AF converter is an open-source application designed to translate the Process Description (PD) format to the Activity Flow (AF) format of the Systems Biology Graphical Notation standard.

Example highlight

ERK signalling


SBGN-MLNewt

SBGN-MLNewt

Conversion 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.