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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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I use Citar (along with the Vertico+Marginalia+Orderless stack) to insert/manage inserting citations and citar-org-roam to take longer-form notes on papers with org-roam.
I have the Better BibTeX plugin in Zotero installed, which keeps ~/Research/refs.bib up-to-date with my entire Zotero library.
I use Citar (along with the Vertico+Marginalia+Orderless stack) to insert/manage inserting citations and citar-org-roam to take longer-form notes on papers with org-roam.
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.