How can-I represent multi-compartment reactions without multiplying the (ugly) compartment boundaries?
All Entity Pool Nodes must belong to a compartment. It is possible to draw an EPN overlapping a compartment boundary, and software may provide magnet tools to implement that. However, the EPN always belong to the compartment containing the center of its bounding box. This is suboptimal, and for many biological processes, we want to use a true compartment to represent a membrane. The problem then is the multiplication of the boundaries. Indeed the membrane would have two boundaries, and each of the adjacent compartments another one. The resulting drawing is ugly, and actually misleading for the non-SBGN expert, who may be induced to think there are many more membranes than in reality. The trick is to use the fact that, in SBGN PD, compartments may overlap as far as no nodes or edges are hidden behind a compartment. The following image represents the conceptual view of the production of ATP by mitochodrion, as shown on figure 14-10 of Molecular Biology of The Cell, 4th edition. However,
