Work flows to interact with books / papers

Hi, I am looking for ways to read a book or paper and record my interactions with it. I am phrasing it like this because I don't want to limit ideas too soon and I don't really know the words to describe it more precisely. The goal is to not only read a document but to make its information more accessible by - for example - highlighting and linking internally and annotating (thoughts) . But I also stumbled upon concepts like transclusion in emacs. This would allow workflows where the document is included into the annotations, instead of the other way round. So my question is: Do you have a work flow to share that enables you to interact wit documents and record those interactions with the help of emacs? Some of my documents are in pdf format, others I have converted to org format.

Something like a Zettelkasten (e.g. Org Roam with bibtex support)? I have a collection of notes, some of which are link to a bibliography.

Hej Hej, I am currently working on a proper workflow for myself. My current status is the follows: I use pdf-tools and nov.el (I mainly read papers and books) to open the files and I use org-noter to write some notes. For other notes I use simple org files that are in different directories according to the subject. All notes and documents are in one top level directory. That is all in regards of packages. Additionally I wrote some functions to print a table of contents for all files in my one directory. All entries are links so I can quickly open them. That is it. Cheers!

org-notes is a thing

org-capture is what you need. Define a good capture template, with the chapter number / progress set up as org properties, and the highlighted text in a quote block. You can later use org-roam, zettel or whatever to refile your notes.

org-noter, but i find the interaction bad. So I just use it for the extracting the PDF's outline tree/skeleton to the respective org file, and annotating in the respective heading. my workflow also includes zotero, org-cite, org-cite-csl, citar, org-roam, org-roam-bibtex, bibtex-completion, pdf-tools, nov.el, org mode capture templates.

If I'm reading books or papers with the purpose for presenting it to a small group, I actually like taking notes within the file that I'm presenting and comment out notes that are less important as I go through the texts. For example, I'll start making a presentation in LaTeX with AUCTeX, I'll describe ideas that I found noteworthy. Toward the end when I'm reading the presentation I'll export the BibTeX file so that I can put the citations in the footer of each slide or in references slides at the end. If I'm not sure whether a source is as relevant, I'll take notes in org-mode and as some of the others have mentioned, I'll write the section names and write an enumerated list of notes under each section. The reason I don't annotate notes in the PDF is it's much easier to `C-s` search a single org-mode file which acts as my notebook when I'm trying to remember what I read a few weeks ago. If I have to read a lot of sources, I won't spend time taking exhaustive notes. I'll maybe track the relevant keywords, or add the sources to a citation manager like Zotero with 1 or 2 sentences about why I think I may need to get back to those sources.

A little out of date, but [this video](https://www.youtube.com/watch?v=Wy9WvF5gWYg) of `org-roam-bibtex` might be of use.

>org-noter, but i find the interaction bad. Same. I don't like how it puts read-only property as I find it jarring. It also messes with the indentation level. So now, I just made a command that uses org-capture to insert the note. I can post it later today if you want me to, tho it is very specific to my workflow.

>a command that uses org-capture to insert the note. I can post it later today if you want me to, tho it is very specific to my workflow. you mean you select the content in the pdf and it copies it to the current frame note (the one side by side with the pdf you taking notes from) or you have to specify the note manually like in a org mode capture template? i was looking into https://emacs.stackexchange.com/questions/51942/how-can-i-capture-selected-text-in-a-pdf-view-buffer-with-org-capture#51943 but the solution isn't as automatic... If you could share your one that would be pretty nice

I'm not sure what you want by "automatic" but my command simply queries you for the heading of the note then puts you in an org-capture note. Since this relies on org-capture in the back, you can take advantage of org-capture. To be clear, this is sort of the what the keysequences goes like, 1. i ;; invoke the command 2. Type in the heading for the note and hit RET. 3. Type in the note. ;; in the org-capture buffer 4. C-c C-c whenever you want to finish. 5. Back to reading. All this time, the pdf buffer will be still in view.