org-noter VS logseq

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.

Logseq support via our Logseq Plugin

Sorry, but _what exactly_ «it seems to do» from your point of view?

My «second brain» now is almost 300Mb of text, pictures, sound files, PDF and other stuff. As I already mentioned, it contains tables, mathematical formulae, sheet music, cross-references, code samples, UML diagrams and graphs in Graphviz format. It is versioned, indexed by local search engine, analyzed by AI assistant and shared between many computers and mobile devices. And (last but not least) it works: it allows me to solve my tasks way more faster than with the assistant of external, non-personalized tools (like ChatGPT, StackExchange or Google).

I know no tools for all this tasks except org-mode. Well, maybe Evernote in the 2010-s was something similar — but with less features, with more bugs and with worse interface.

Personal note-taking _is_ a complex task per se (well, at least for someone like typical HN visitor). I've seen many note-taking tools, that were ridiculously featureless, stupid and inconvenient because they were _not_ complex enough.

> Sure if one wants to do emacs-gardening it is fine.

1)You can use org-mode outside Emacs. See for example Logseq (https://logseq.com/), organice (https://organice.200ok.ch/) or EasyOrg.

2)Org-mode works in Emacs out of the box, you don't need any «emacs-gardening» to use org-mode.

3)The term «Emacs-gardening» itself sound a bit like hate-speech for me. The complexity of Emacs customization is overrated, mostly due to opinions of people who never used Emacs or used it in the previous millennium.

Obsidian is great.

For those looking for an open source alternative (or don't want to pay the Obsidian fees for professional usage) check out Logseq: https://logseq.com/

For an opensource alternative to Obsidian checkout Logseq (1). I spent a while thinking obsidian was opensource out of my own ignorance and was disappointed when I learned it was not.

1: https://logseq.com/

I use logseq to keep journal of my daily work.

While Emacs and Org mode can certainly be used for this (and, when they can't, you can always inject little python/js scripts in your emacs config to take care of specific things), I'd also recommend you take a look at Logseq.