Also there's Zim wiki [0] which runs on the desktop. I use it to create a ton of notes and knowledge piles.

Zim's UI looks more dated and simpler, but underneath it's extremely powerful.

[0]: https://zim-wiki.org/

+1 for Zim.

The UI is utilitarian, simple and efficient. It stores all of its note files as .txt so there's lots of other ways to access the info (e.g. grep).

Zim is extensible with a variety of useful plugins too.

I use it with the plugins enabled and, it helps a great deal for my knowledge organization and acquisition.

Its simple file structure also allows me to pair it with syncthing [0], and sync all of my computers with each other seamlessly. So I have my own self-syncing document trove and knowledge base without any considerable effort.

Using simple apps and integrating them is much more powerful than it looks, and it's one of the simpler things that I enjoy immensely.

[0]: https://syncthing.net/

And Trilium also supports synchronization (though it would be more awesome if it would work decentralized like git).

I'm somehow not very comfortable putting my ideas or research into some graph db I don't own.

Trilium synchronization is "decentralized" in the sense that each instance (server, clients) has full copy of all the notes and metadata.

Ok so it's decentralized, very nice. Probably I misunderstood their sync-model when I saw the star shaped network with a central server.