org-pdftools VS org-noter

An alternative is to open PDFs, from Zotero or from anywhere else, with Emacs' pdf-tools (https://github.com/vedang/pdf-tools). If you annotate the pdf, those annotations are part of the pdf. And you can also use org-noter (https://github.com/weirdNox/org-noter) and org-noter-pdftools (https://github.com/fuxialexander/org-pdftools; but see https://github.com/fuxialexander/org-pdftools/issues/93#issuecomment-1493314118 if you use the new org-noter from https://github.com/org-noter/org-noter).

Periodically, I go through the pdfs I've read (I have a collection in Zotero for the stuff I am in the process of reading) and I use org-noter-pdftools (see https://github.com/fuxialexander/org-pdftools ; this is different from, and extends and depends on, org-noter which, by the way, has recently got new maintainers) to extract all annotations in the pdf to a note that is associated to each pdf. One to one mapping here: one pdf file - one .org file for notes. These notes are basically just org(-roam) files that store the annotations for easy searching (see below) and to allow my linking to specific, individual, highlights (or text annotations). I think that initially setting everything up to my satisfaction was a little bit confusing (e.g., the names of some functions I think are the same between org-noter and org-noter-pdftools and sometimes it was unclear to me the differences in functionality between the two packages); but now it works flawlessly. From org-noter-pdftools I specially like how easy it is to get all the highlights, text annotations, etc (not manual scribbling, of course, and see also below for "typewritter" annotations) into an org-roam note that links directly to the exact location in the pdf.

Check out my screencast on org-noter. I don't think anything else comes close to this kind of workflow. Unfortunately it's not production ready yet. There's a related project org-noter--pdftools, I don't recall what it's state is.

First I tried config from here - https://emacs.stackexchange.com/questions/19686/how-to-use-pdf-tools-pdf-view-mode-in-emacs but the package in unmaintained, so I used https://github.com/fuxialexander/org-pdftools

[2] https://github.com/fuxialexander/org-pdftools

I regularly paste text from other sources (e.g. a bit of Wikipedia text for a stub note, or highlighted text from a PDF via org-noter) into my notes and what I am looking for is a way to find/indicate existing org-roam entries in those pieces of text.

So right now I am having to go through tons of reading material. I'm taking an abundance of notes, etc. I'm trying to prep for an exam. I need to read multiple books, and I just started with the first one. I opened PDF-tools and then, using Org-noter I started taking notes. Each note is like an annotation in the book, tied to its specific location. Next time when I go through my notes, I can jump to the specific page in the book. And vice-versa - while re-reading through the book, I can see all related notes, right there in the adjacent window.

First, make sure that you are using this repo, instead of the other one which is unmantained for a couple years. It includes a lot of fixes and new features that with luck might fix your issues.

Thank you for your detailed answer - I am not OP but I just wanted to point out (in case you were unaware) that the great org-noter has recently found a new maintainer and the repo has moved here: https://github.com/org-noter/org-noter

An alternative is to open PDFs, from Zotero or from anywhere else, with Emacs' pdf-tools (https://github.com/vedang/pdf-tools). If you annotate the pdf, those annotations are part of the pdf. And you can also use org-noter (https://github.com/weirdNox/org-noter) and org-noter-pdftools (https://github.com/fuxialexander/org-pdftools; but see https://github.com/fuxialexander/org-pdftools/issues/93#issuecomment-1493314118 if you use the new org-noter from https://github.com/org-noter/org-noter).

The maintained repo is at https://github.com/org-noter/org-noter and the branch you want is https://github.com/org-noter/org-noter/tree/bugfix/nov-mode.

Possibly: Org-noter and/or PDF Tools.

New version on melpa; new repo at github.com/org-noter/org-noter

If you have un-dealt-with PRs on the author's repo, please redirect/resubmit them to https://github.com/org-noter/org-noter.