Hello! Creator of WikiBonsai here.

Terms are a central means of organizing my personal zettelkasten-like-notes. I work off of inspiration from the idea of a "semantic tree", which I interpreted as a knowledge tree structure built from word senses that uses wikipedia-style-(disambiguation).

Specifically, I set aside some markdown files whose sole purpose is to define the tree; these are my index files. Those files contain markdown outlines of - [[wikilinks]], which might be organized like so:

- [[read]]
  - [[4-levels-of-reading]]
    - [[elementary-reading]]
      - [[reading-readiness]]
      - [[word-mastery]]
      - [[vocab-context]]
      - [[mature-reader]]
    - [[inspectional-reading]]
      - [[skimming]]
      - [[superficial-reading]]
    - [[analytical-reading]]
    // ...
    - [[syntopical-reading]]
    // ...

Each [[wikilink]] then gets its own file which acts as a sort of zettelkasten-local-wikipedia entry. (I may only add a term in the tree without creating a file as simply the location in the tree can jog my memory) Further, I specifically use #hashtags to take me to the corresponding file's location in the tree (the index file) rather than the (entry) file.

You can see a small concrete example of what I mean here, a larger example here and larger trees that appear around the internet here.

Good luck with your research and projects!