Reference Management Apps: A Review

Recently I tweeted about reference management apps to learn what people preferred. I saw several different answers, so I decided to check them all out and decide what I preferred.

What is a reference management app? It’s software that helps you keep track of scientific papers you’re reading, and can manage and format your citations for manuscripts. I’m deep in a massive literature review right now, and I’m looking for software that can help me organize and keep track of what I find, and ultimately help me cite these papers later.

There are a lot of software options out there, so I just checked out the ones I saw people talking about on Twitter: EndNote, Mendeley, Papers, and Zotero. Here are my impressions.


I went to the EndNote website and found out it was $250 with no student discount or trial version available. My investigation ended there.


I went to the Mendeley website and made an account through Shibboleth, logging in with my academic institution. That was fine. Then I downloaded the desktop app, and suddenly I couldn’t log in because I had chosen to make my account through my academic log-in. I would have to delete my account and start over with a non-academic log-in to get the desktop app to work. I decided this was incredibly clumsy and poorly designed - why offer a log-in option that only works for the limited online version of Mendeley? - and gave up.


In theory, Papers would be my ideal reference management app. You can search a dozen databases for papers from the app and import them and their full texts to your library. The interface for reading and annotating papers is beautiful. It keeps track of which papers you’ve read and which ones you haven’t yet. There are so many shiny features.

In practice, Papers was very glitchy. It often crashed when I tried to open certain features. It kept mislabeling which papers I’d read or hadn’t, and reading in metadata wrong. Most of the database search engines didn’t work. Worse, the help files are very sparse and provided no solutions to any of these problems. If Papers worked exactly the way it’s supposed to, I would happily pay the license fee. But it didn’t work that way at all.


Zotero is the only one of the options I’ve reviewed here that is open source, a major advantage. It has a simple interface on the desktop app, a series of folders you can organize your papers in with links to the PDFs, and its system for generating citations plays nice with just about everything. Zotero comes with browser extensions you can use to import any paper you find in your browser into your library, PDFs and metadata and all. And if you have any problems with the app, there is a thriving online community developing this open source software.

Zotero, to me, is clearly the best reference management app available. It’s free, open source, and it just works. I wish it had some of Papers’ features, but Papers doesn’t even have those features, since it glitches so much.