The GPML data models allows linking data nodes with interactions, or an interaction with another interaction. For example, an enzymatic reaction has two interactions; one between two metabolite nodes, and the second between the enzyme and the first interaction.
An interaction that does not connect two entities properly via the interaction’s start and end point, is called “unconnected”. These unconnected points (i.e. ends of interactions), limit how efficiently the pathway can be used in, for example, network analysis.
Ideally, all interactions connect to other entities. The fail signals that this is not the case.
The interaction should be looked at and should not have unconnected points.
In PathVisio 3.3, you can use the Ctrl-L functionality to highlight in green the unconnected points.