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citar
Emacs package to quickly find and act on bibliographic references, and edit org, markdown, and latex academic documents.
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Then, install 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.
First things first, install pdf-tools, a great Emacs package for viewing pdfs. The default pdf viewer Docview is very limited so you should definitely get this package.
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 and bibtex-completion (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.
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 and bibtex-completion (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 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 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.
Taking this one step further, if you use the excellent 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 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.
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.