I was just curious. It seems you use your PKMS to do scientific inquiry. Sure it makes sense 
I use other entities, less scientific, such as question, opinion, conversation, etc.
When I use the PKMS to work as an engineer, I connect entities such as people, drivers, goals, outcomes, principles, requirements, planning, software artifact, etc.
I use relations such as ‘is a’, ‘supports’, ‘requires’, ‘belongs to’ that help me to track actionable items.
How do you do the diagram?
Do you use the breadcrumbs plugin?