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If it's text-heavy I'd recommend Obsidian

So the goal would be to eventually move that graph into running code and query it. But it’s never going to be large - easily fit in memory.

Obsidian is PKM right? Does it have the idea of labels on the edges?

Right, in that case Obsidian might not be the best choice.

I'd look for Knowledge Graph editors then, for RDF or OWL knowledge bases, I don't have any specific recommendation, there are many but most are rather old.

Alternatively, go for a graph database like Neo4j, it's primarily designed as a database and not an editor, but it does have a nice UI visualize and change things by hand.

https://schematix.com

dot/vimdot/graphviz promises to do it but I was not able to get it to work yet