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deepig's Org-ref Workflow
Sneaking into the Libary

Table of Contents

knowledge-quest.jpg

Figure 1: Knowledge Quest

In the spirit of building on the shoulder's of giants what follows is a series of posts's by reddit user deerpig on his workflow with org-ref. I found it very helpfull and an inspirational use of free software. His incorporation of sci-hub and libgen into the flow is very interesting and might serve as a guide to how institutions in developing countries can get access to solid research without supporting what he calls the academic publishing mafia.

His other posts are also well worth checking out.

deerpig's Org-ref workflow. Taken from a series of posts on reddit.

Org-ref is not buggy and despite appearances the documentation is good. But it does take some thought to set up. It is well worth it. It is my daily companion – together with helm, bibtex mode and PDFView. Give org-ref a DOI number and it inserts the bibtex entry. Cambodian higher educational institutions don't have much in the way of libraries, let alone budgets to pay rents to the academic paper. Combine that with one of the notes packages that work with PDFView and you can link notes to specific pages in PDF. Save it using the BibTeX key and org-ref pulls up the PDF using PDFView. It's an astonishingly powerful combo and you are selling yourself short not putting a little effort into publishing mafioso, so LibGen and Sci-Hub are our life-lines. Feed sci-hub a DOI and you get a getting it setup and part of your workflow. Seriously, Org-Ref should be thought of as in the same category as Org-Mode, Magit and Helm/Company. I suggest that you create your own BibTex Yasnippets – the ones provided out of the box with BibTex mode AND the ones that come with Yasnippets don't

cut it. I'll be happy to create a Gist with the snippets if anyone is interested. John Kitchen deserves an Emacs Knighthood. Henceforth I shall refer to him as Sir Kitchen :)

Quotation 2

I use the Helm BibTeX interface to browse and insert citations. And this is where it can get tricky, because some things are governed by Bibtex Mode and others by Org-Ref and there are a few places where they don't work well together. When you are using the Helm interface you are in BibTeX mode and that mode governs what you can do. But once you have inserted a citation into a document you are in the org-ref domain which does things a little differently. Some things you just experiment with. Inserting bibtex entries from DOI numbers took me a few tries to work out. But if I was able to work it out, I'm sure anyone can.

Quotation 3

I have a set of custom interactive yasnippets to create new entries from scratch in the rare instance that there is no doi number, the book is not in libgen as a last resort is also not in Google Scholar (I recommend installing the Google Scholar Plugin for Firefox or Chrome).

For books, I've found that the bibtex entries by libgen are far better quality and formatting than what you get from Google Scholar. When you find the book on libgen go to the page for the book and look on the right side for a link called "link" this takes you to the bibtex entry for the book. I especially like that most entries include isbn numbers.

Of course you can also download the book from libgen, and use doi or jstor numbers to grab papers from sci-hub. Our school doesn't have the budget to subscribe to any journals. In fact there is a good chance that there are no libraries in the country who subscribe to journals, so libgen and sci-hub are our only means of accessing books and papers. I know people in other countries who have full access to journal subscriptions who still use the same approach I use to add books and papers to their bibtex database. It's faster and easier.

Quotation 4

Org-ref is your best friend forever. The joy of calling M-x doi-insert-bibtex instreat of spending ten minutes creating a bibtex entry by hand is hard to beat. Org-ref can download and open the pdf of the paper as well, but only if you have paid access. What I do instead is highlight the doi number and call a shortcut to sci-hub using engine-mode, which then opens the pdf in my browser. I save downloaded pdfs using the bibtex id so if I need to read the paper again org-ref will open it in emacs.

Method

  • Give org-ref a DOI number and it inserts the bibtex entry.
  • Run doi-insert-bibtex give it a doi number and a beautifully formatted bibtex entry is inserted. It's not uncommon for me to add 30 or more papers and books to my bibtex database a week, so this is a big time saver.
  • Once you have inserted the bibtex entry, since I have no access to journals through our university you can grab the paper from sci-hub. Since org-ref doesn't look for papers on sci-hub I use engine-mode (https://github.com/hrs/engine-mode) to create shortcuts to sites that DuckDuckGo doesn't have Bang shortcuts for, including torrent sites, libgen and sci-hub. So all I have to do is:
  • M-x doi-insert-bibtex
  1. Paste the doi at the prompt hit <enter> and the bibtext entry is inserted.
  2. Now highlight and copy the bibtex key (which I use as the name for the file so that org-ref can easily open the paper using pdfview).
  3. Finally, highlight (but don't copy) the doi number in the entry and press C-x C-/ h (you'll have to add it to the keymap) and the paper and it will open in your browser.
  4. Feed sci-hub a DOI and you get a paper
  5. Combine that with one of the notes packages that work with PDFView and you can link notes to specific pages in PDF
  6. Save it using the BibTeX key and org-ref pulls up the PDF using PDFView
  7. I suggest that you create your own BibTex Yasnippets

For books, I've found that the bibtex entries by libgen are far better quality and formatting than what you get from Google Scholar. When you find the book on libgen go to the page for the book and look on the right side for a link called "link" this takes you to the bibtex entry for the book

Author: balticman

Email: david@geffle.se

Created: 2022-02-14 Mon 15:00