Testing
In the SBGN PD standard format, a process glyph is represented by a square box linked to two connectors, small arcs (“antennas”) attached to the centers of opposite sides. These are denoted as ports. The incoming and outgoing arcs linked to a process glyph connect in reality to the port of that process glyph.
In the yEd Graph Editor (https://www.yworks.com/products/yed), there is no dedicated support for such “ports” currently. Thus, the incoming and outgoing arcs are directly connected to the process, without ports. In order to represent the two small “antennas”, the user has to add bend points on the links.
Figure 1: The SBGN process glyph vs. the yEd process glyph.
In black are represented the process glyph (square box) and the ports (black line). In red are represented the incoming and outgoing arcs. The SBGN process glyph connects to these arcs through the ports which is represented by the two black lines on each side of the square box. The representation of yEd of a process does not take into account ports: the incoming and outgoing arcs are directly connected to the process square box.
The process port assignment can be tested using the ProcessPorts file available for download here.