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A PhD Examined: Reference Management Software

How I Efficiently Managed the Articles I Used in My Research

Joe Riad
6 min readNov 10, 2024

By its nature, research work requires you to do a lot of reading. You read articles, books, white papers, lectures, etc… All these reference sources contribute to your education and over time and with repetition, you internalize what you learned and forget where exactly you read about it. This was my way of thinking when I started grad school. The problem with that, of course, was that I was also required to give proper credit when I cited someone else’s ideas in my own articles. In some cases, I had to cite articles I had read a few years earlier and it was quite hard to keep track of all the references I had read.

Reference management software does exactly what its name implies: it helps you keep track of your references and lets you cite them easily. Unfortunately, I only discovered and started using reference managers late in my PhD program. Because of that, this article will not have many anecdotes from my personal experience. Think of it more as a cautionary tale: “learn from my experience and use a reference manager from the start”.

My Experience

I had heard of reference managers early on during my master’s program but didn’t bother using one for several reasons:

  • I thought I could keep track of the things I learned in my head
  • I was writing my articles in LaTeX and using to format my citations. It also acts as a mini database to collect all references in one place and make citing them quite easy.
  • I was working on one topic in my master’s program so the number of ideas I read up on and explored was limited and the scope was narrow.

When I started on my PhD, I thought that things would continue pretty much the same way. I figured that even if I was going to work on multiple projects, I would finish one and write all the articles detailing my work on it before starting another project. The reality of my work turned out to be quite different. I was reading many articles and being exposed to a lot of different ideas. My work on different projects was interleaved and I had to sometimes stop working on one project to focus on another, more urgent one. Articles and books I had read for a class were suddenly becoming relevant to an article I was writing a couple of years down the line. I needed to keep track of all these different ideas so I could easily return to the source if I needed to refresh these ideas or to cite them in my own work.

By that point, I had forgotten about most of the capabilities of reference managers and only remembered that they were something I had looked at and decided I didn’t need. It didn’t occur to me that the reasons I rejected them earlier no longer applied to my situation. I even toyed with the idea of writing my own little program that allowed me to link ideas from multiple papers so I could find them quickly. This never amounted to anything, of course, because I didn’t have the time for it.

The breaking point came when I started working on a review article near the end of my program. Review articles naturally require you to read a great number of articles and summarize and crystallize the ideas from this reading into a message of your own. I ended up citing about 70 articles in that work but probably read about 100 different articles on this topic. I had to read these articles in the span of a few months and keep track of the ideas in them so I could cite them correctly. A this point, I decided I needed to use a reference manager.

Software Overview

I will briefly go into the features of a few reference managers. Most of these are applications I haven’t used myself but know of them and/or know people who use them. In my opinion, a good reference manager should let you search your references to quickly insert a citation into your document, should allow you to take notes on any references and should make the notes easily searchable. These are the criteria I will use to evaluate each of these programs.

Mendeley

  • Supports annotations and highlights on PDFs of your papers
  • Browser plugin to import a paper you’re viewing online
  • MS Word add-in to insert citations in a document
Screenshot of the Mendeley interface from the Mendeley website.

Pros

  • Available cross-platform
  • Free to download

Cons

  • Free plan only allows you 2GB of storage (may or may not be enough depending on the number of articles you plan to store)

EndNote

  • Supports annotations, highlights, and searching in PDFs of your papers
  • Browser plugin to import a paper you’re viewing online
  • MS Word add-in to insert citations in a document
  • Can create your own custom citation style
Screenshot of the EndNote interface from the EndNote website

Pros

  • Free to download (30-day free trial)
  • Quite popular, your university will have likely bought it for students

Cons

  • Desktop client is only on Windows and Mac, no Linux support
  • Requires a monthly subscription if your university is not paying for it
  • Interface may be a bit complicated

Zotero

  • Supports annotations, highlights, and searching in PDFs of your papers
  • Browser plugin to import a paper you’re viewing online
  • MS Word (and LibreOffice Writer) add-in to insert citations in a document
Screenshot of the Zotero interface from the Zotero website

Pros

  • Available cross-platform
  • Free to download

Cons

  • Free option only gives you 300MB of storage
  • Phone app only available for iOS

JabRef

  • Supports searching in PDFs of your papers (doesn’t seem to support annotations)
  • Search feature does not search in annotations
  • Browser plugin to import a paper you’re viewing online
  • MS Word (and LibreOffice Writer) add-in to insert citations in a document
Screenshot of the JabRef interface from the JabRef website

Pros

  • Available cross-platform
  • Truly free

Cons

  • Functionality might be limited compared to other managers
  • No phone support

org-ref

This one is a bit special since it’s lacking a bit in the functionality department. It should probably be called a citation manager rather than a full reference manager.

I’m including it here because it’s the approach I ended up using. It’s a free and open-source extension to the Emacs text editor and it only supports inserting citations into Org documents in Emacs. This worked for me as I was already using other extensions of Org to take notes on my PDFs and search through them. Think of this extension as a frontend to search through the citations database created by Bibtex.

  • Only supports inserting citations and searching through them
  • Only works in the Emacs text editor
Screenshot of the org-ref interface showing a search for citations (from the project’s Github page)

Concluding Thoughts

Having a reference manager is essential to wrangling the complexity and sheer number of articles you will be going through in grad school. There are many reference manager options and I encourage you to explore them a bit on your own (and maybe find others I don’t know about) until you find the right fit for you.

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