Hey! I came across your post and totally understand the frustration — the global graph becomes unusable once your vault has enough interconnected notes.
I ran into the same problem, so I built obsidian-graph-query — a skill that lets AI coding agents run targeted graph algorithms directly on your vault’s link structure via
Obsidian CLI. Instead of staring at the entire vault graph, you query only what you need and get back structured results.
A few examples mapped to your use cases:
- “Show me herbs that cool blood and their connections” — neighbors query starts from a specific note and traverses outward N hops, returning only the related herbs and their
linked actions/formulas - “How is herb X related to formula Y?” — path query finds the shortest connection chain between any two notes
- “Which notes are key connectors?” — bridges query finds notes that are the sole link between different knowledge clusters
Your vault structure (herb → actions, formula → components) is actually ideal for graph queries — the relationships are already encoded as links, which is exactly what the
algorithms traverse.
If you’re using an AI coding agent that supports skills (Claude Code, OpenClaw, Cline, etc.), give it a try. I shared more details here on the forum: