What’s that?
The structure of my PKMS.
AREA, TOPIC, THEORY, and OBSERVATION are notes/files in Obsidian. Each note has a specific tag:
AREA #area
TOPIC #topic
OBSERVATION #observation
THEORY #theory
The relations between notes are dataview inline fields.
Does it make sense?
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?
You are right, this more apt to a scientific body of knowledge. The graph is simple mermaid. You can do it directly in Obsidian.
Yes, I use breadcrumbs, but I’m still struggling with it. I use for instance topic and area inline fields as parent hierarchy. Still I’m wondering if this is not just unnecessary complicating the whole structure. I want to keep things as easy and plain as possible to safeguard applicability to the major possible variety of contexts.