See "org-roam" [1,2] (and several blog posts and youtube videos by now)
[1]: https://github.com/org-roam/org-roam [2]: https://blog.jethro.dev/posts/introducing_org_roam/
Don't miss these additional packages, which build on org-roam:
org-roam-server: better graph visualization and navigation [1]
org-roam-bibtex: Reference management in your Zettelkasten [2]
The latter, combined with org-ref and org-noter, is the most effective way I've found for taking notes on PDFs. Beautiful demo at [3].
FWIW RoamResearch has yet to implement a useful graph view, PDF annotation, or reference management. OTOH, tending to a setup like this in Emacs can easily become a time-sink, and it's single-player only.
[1]: https://github.com/org-roam/org-roam-server
I've started to wonder if the Emacs community should put together versions that are ready for different kinds of users out of the box. Say, a version for scholars with everything Auctex, org/org-roam, spell check, email, rss, etc already there, and a walkthrough to boot. Like a distro or spin, basically.
Here are three I'm aware of:
Scimax: https://github.com/jkitchin/scimax
Emacs Speaks Statistics: https://github.com/emacs-ess/ESS
Frontmacs: https://github.com/thefrontside/frontmacs
So long as these approaches expose the full power of Emacs to their users, I can't imagine the UX being as rock-solid as we might expect from modern purpose-built tools (e.g. PyCharm, Overleaf, Obsidian, ...).
It might help to hide/disable most default interactive functions, which provide a huge surface area for non-Emacsers to break things. Emacs actually does this by default for a few functions: https://www.emacswiki.org/emacs/DisabledCommands
Also relevant here is wakib-keys: https://github.com/darkstego/wakib-keys.