For personal knowledge, most graph-based ideas were pioneered by Niklas Luhmann in his Zettelkasten system. This system is described with lots of detail in [1] and made him extraordinarily productive.

Essentially, Luhmann had one small card per semantic unit. Cards had alphanumeric IDs. Cards backlinked to other cards using said IDs. He also used a card branching mechanism implemented in IDs as e.g. 123 -> 123a -> 123a1 which he called Folgezettel.

Lastly, he also had cards whose role was mostly to connect topics by serving as a link hub.

It's a really simple system that you can implement using plain text, Org, Markdown or some note taking application like Apple Notes or OneNote plus a few conventions.

After trying many things, for personal use I think nothing beats plain text (or a plain text format). I don't need a server, I can easily sync things, and it's really future proof.

I have also scaled this kind of setup to larger organizations, albeit using a more classical wiki-like approach (read longer articles instead of small semantic unit cards). For example, GitLab has excellent continuous integration. You can use an Emacs or Pandoc inside a Docker to export Org or Markdown files into an HTML.

[1] https://takesmartnotes.com/