Write research paper notes/summaries in emacs

I am a beginner in Emacs and I was wondering if there is a way to write research paper summaries with the PDF of the paper open on the side and text (preferably markdown) summary on the other side with references to lines/locations in paper. I currently use Mendeley for general text highlighting and in-line notes but I am looking for adding summaries and reference lines in the Mendeley annotated PDF in Emacs.

Since my 1978-79 freshman year, nearly everything i ever wrote was in emacs and scribe/TeX markuo

I wrote a series of articles on how to do research in Emacs: https://lucidmanager.org/tags/emacs/ Org roam has Bibtex support, so it creates a nice annotated bibliography. :Perhaps useful for you.

You might want to have a look at https://github.com/weirdNox/org-noter (there's an outdated screencast in there, but it shows the main features).

org-noter + pdftools is what you are looking for. you can keep precise notes in separate org files with the option of imbedding your notes into pdf directly.

I would personally argue that Emacs is one of the best tools out there to do this, I myself do this extensively using Emacs. First things first, install [pdf-tools](https://github.com/politza/pdf-tools), a great Emacs package for viewing pdfs. The default pdf viewer Docview is very limited so you should definitely get this package. Then, install [org-noter](https://github.com/weirdNox/org-noter). Org-noter is another very powerful Emacs package which gives you the ability to annotate your pdfs in a separate org-buffer. It has many capabilities and is ideal for annotating articles. You can choose where the note points to and then write your summary about it in the side buffer that opens. The headings org-noter creates are then kept there and you can always go back to them and see where in the pdf they point. This on its own is a great system for writing such notes. However, it is very lacking in searchability. If you want the notes, you need to go find them. To solve this, you first need a package to manage your bibliography in Emacs. These function with a .bib file that I assume you already can obtain through Mendeley. To my knowledge, there are two great packages for this, [citar](https://github.com/bdarcus/citar) and [bibtex-completion](https://github.com/tmalsburg/helm-bibtex) (which is actually two packages ivy-bibtex and helm-bibtex). Depending on the completion framework you are using (Ivy, Helm or Vertico/Selectrum) you can use one of these. These packages read from a bibliography file and make your life so much easier in finding the research paper you are looking for. They also have another neat feature. They allow you to create notes for your bibtex entries with ready customisable templates. This makes this whole process so much easier as you can find a paper you want to read, create a note for it with one of these packages and then link it to its pdf with org-noter. This way you have a fully-fledged research workflow inside Emacs. Taking this one step further, if you use the excellent [org-roam](https://github.com/org-roam/org-roam) package (which if you don't you should definitely check it out, its great for note-taking), there is a package called [org-roam-bibtex](https://github.com/org-roam/org-roam-bibtex) which communicates very well with the aforementioned packages. With it, you can create bibliographic notes as part of your org-roam repository from their bibtex entry and initialize the file to also include a link to the pdf from org-noter. Once you learn it, its a very powerful and streamlined workflow for working with articles which makes your life very easy. Its quite a bit of reading to do on your end on how to make all these work together, but trust me its worth it. Also a quick mention to my own workflow which uses all these which you might find helpful as a starter kit. I recommend you read this after you get a feel of what the packages do as its not gonna be so in depth. First, make sure all your pdfs are stored in the same location and are named something sensible (ideally make them similar to the citekey). I don't know how to do this in Mendeley as I use Zotero personally. Once you have this, org-roam-bibtex should recognize all your pdfs and be able to match them to their bibtex entries through their citekey. With this, you can make a capture template specific to bibtex entries that stores important data for the entry in the org-file and that also adds a heading which knows to find your pdf automatically and set up org-noter with it. This way, when you initialize such files, you can automatically have org-noter ready with the correct pdf. I use this template for that which is a slightly modified version of one that is in the wiki of the package ``` ("r" "bibliography reference" plain "%?" :if-new (file+head "ref/${citekey}.org" "#+title: ${title}\n #+filetags: ${entry-type} - keywords :: ${keywords} - tags :: * Analysis of ${entry-type} by ${author} :PROPERTIES: :URL: ${url} :NOTER_DOCUMENT: ${file} :NOTER_PAGE: :END:") :unnarrowed t :jump-to-captured t) ``` This will basically get everything ready for you when making your files. Then I would personally also recommend making the ivy-bibtex (or helm-bibtex) default action to be creating a note with this snippet `(setq ivy-bibtex-default-action 'ivy-bibtex-edit-notes)` There is definitely a way to do this in Citar which should be mentioned in the wiki if you read through it (and if there is not the author of the package is very helpful in general) but I do not know what that is. This way, when you select a bibtex entry it will automatically create a note with the title being the title of the article, automatically associate the entry with its pdf and ready org-noter for use to annotate it. Its a very streamlined and automated way to work with this system of packages that I highly recommend. For more info on this, you can also look at my literate config for notetaking which naturally has a lot as I take tons of notes. Link to it is [here](https://github.com/Vidianos-Giannitsis/Dotfiles/blob/master/emacs/.emacs.d/libs/zettelkasten.org). That's all I have to say. I know its a lot to digest but read it in your own pace together with the documentation of the packages (which is great for all the ones I mentioned) and I am sure you will love this workflow once you figure it out. That's all for me, if you have any questions feel free to ask.

Isn't org-noter outdated itself? My biggest issue with it was the lack of 2 column paper support. That being said, your recommendation is spot on. To the best of my knowledge this is the best/closest thing in emacs to what OP was asking for.

This is an excellent suggestion. Definitely something I was looking for. I'll give it a go. Thank you for the recommendation.

Is it outdated? Is there any recent package that has replaced it or provides similar if not all features? Most of the research papers I read are 2 column papers so compatibility with 2 column papers is a foremost requirement for me. Let me know of any other alternatives. Thanks.

Thank you I'll take a look. The articles on the link you shared will be very useful for me to get more out of emacs. Cheers!

Yes, embedding notes directly into the pdf is a very attractive feature.

Skimmed through your emacs files on GH and have to say one of the most well organized configurations I have seen. And, much too copy from ;)

Hey man I appreciate it. My config sometimes feels like a big mess to me however 😂, but I have put in hours to make it have a good structure in an org-document so it's easier to read so I am happy ypu found it helpful. If you have any questions about it I would be glad to help you.

Ah, that feeling explains the urge for structure ;) I was wondering if you consider creating a bibliography org file which will then be tangled into a bib file. I like that idea because one can add annotations to the references.

I have seen that idea explored in the past by others and not gonna lie it is a good one. The problem I have with an Emacs only workflow for bibliography is that it makes capturing harder. I typically manage bibliography with Zotero which gives me a bib file for Emacs. Capturing in it is one button and furthermore, it allows me to organise my bib entries in some way. Emacs definitely can get better organisation with org and allows for easy annotations on each entry, but the problem I have with it is I am not aware of an actually fast way of capturing immediately to Emacs and doing it manually would be a pain