Annotating non-Org documents (primarily PDFs)

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A bit rambly, sorry. Summary: As someone in a similar situation, if it's PDFs annotations, I think the simplest solution would be to use a tool you're comfortable with to annotate the PDF (e.g. Zotero, pdf-tools), extract those annotations as plain text, then org-attach/link/org-transclude them to the relevant nodes in your org roam directory. Not a good enough programmer to automate it, but I'm sure it's possible lol. I ended up moving a lot of my pdf annotating out of emacs and into Zotero, since Zotero does most of what I need. Longer: If memory serves, I was able to export annotations from the Zotero database to the PDF, then use org-noter to extract the annotations. The issue I had was it would fail on some PDFs. The solution I found was to export those annotations to a note in Zotero, then export the bibliography with annotations stored in some section, then use org-roam-bibtex to extract the entries into nodes. I actually made an additional step where I had the bibliography node for summary and the notes field transcluded into it from a separate file, using org-transclude. Biggest issues were that it 1. was a lot of steps 2. made the bibliography rather hard to navigate 3. created annotations that weren't nicely formatted. I haven't played with this in a couple of months, since just using Zotero's native annotation features and sometimes copying notes to org files is enough for me right now, but it might be a good basis. Also I have a bigger screen, so can more easily read a text in one window while writing comments in another lol. Also if you're annotating plain text, [org-remark](https://nobiot.github.io/org-remark/) is great. I love not having to use the mouse to select text. There's also a [pull request on the new pdf-tools](https://github.com/vedang/pdf-tools/pull/29) that allows one to use the keyboard to select text as well. I don't think it has been added to the project yet and when I pasted the code into my init.el, it didn't work well (highlight not on text), but it is apparently a milestone so hopefully something will come of it.

I use the package org-noter.

I do the same. Paired with ivy-bibtex and org-ref, it is a good combo for me. I think there is a way for notes to be integrated in org-roam but haven't looked into it enough.