One of the most important tools in any researchers toolbox is the reference manager they use. What is a reference manager? A program that lets you collect, store and use the metadata associated with the books, papers and other sources you read for your research.

In the olden times, before computers did this for use, this was done using manually typed index cards, like you see in Figure 1. Thankfully, reference managers (you'll also see them called citation manager or bibliography manager) today give us many more affordances than a paper-based system.

But why should you use a reference manager in the first place?

One of the things that distinguishes writing in academia or adjacent fields from writing in the news or on blogs like this one is that you are required to give exact citations for any source of information that you reference. It's not okay to just say "a recent study found that X", you need to provide detailed information on who conducted that study, when and where it was published and, when you're quoting specific results or claims, on what page they were made.

That requirement is cumbersome, but essential: otherwise it would be extremely difficult if not impossible to verify assertions and track the provenance of ideas.

In practical terms, it means that you need to collect the information about the paper or article you're reading as soon as possible and store it in a central and easily accessible place. Otherwise you'd have to look up this information later, most likely repeatedly, and that's way too inefficient once you've started really digging into a field. Looking at hundreds or even thousands of papers over a career is common, and you don't want to do the same thing twice when that's the case. Hence, use reference managers. And use them earlier than you think you need to: even managing the sources for a single seminar paper in undergrad is worth the small effort it takes to set up a reference manager.

In fact, I would recommend you use a reference manager even if you're not in academia at all. A good reference manager can actually be a pretty nice bookmark solution as well, and it's always a good thing to have all relevant information about a source at hand when you're looking for it.

With that out of the way, let's look at what exactly a reference manager can do for you.

What features should you expect in a reference manager?

The two most important features in a reference manager are that it's easy to get citation data into the app and that it's easy to use that citation data in your writing tool of choice.

Ideally, you want the app also to be as cross-platform as possible and work on Windows just as well as on macOS or Linux, be free, and let you manage the PDFs of papers or scanned book chapters.

In my opinion, the app that gives you all of this and more is an app called Zotero.

Why should you use Zotero as your reference manager?

Zotero is a great, free, reference manager that's extremely good at letting you collect citation data. It comes with a browser plugin that lets you save citation information with one click on Google Scholar, journal pages, and even Youtube, Amazon and many other websites, including news articles. When available, it automatically downloads the associated PDF for a source, which is very convenient, and makes a website snapshot for news articles.

Zotero also has a great plugin for Microsoft Word and Libre Office that makes it super easy to reference a source. With a simple shortcut it allows you to search you whole database of sources, insert and automatically format it according to the citation format you want to use. At the end, it takes care of taking all the sources you referenced in a paper and formatting the bibliography for you – that alone can save you hours of work compared to not using a reference manager.

Another point in Zotero's favor is that it is open source and has some great extensions available. The BetterBibTex extension allows you to add citekeys to each paper and automatically keep a .bib file up to date that you can then use with LaTeX or Pandoc to make citations super easy when you're writing your paper in (R)Markdown files.

The Zotfile extension gives you lots of control over where Zotero stores the PDF files of your papers, and how it names them. That's great when you want easy access to your PDFs on multiple computers and your tablet, without being locked in to a specific software. Zotfile also automatically extracts any highlights you might make, saving you lots of work copy-pasting from badly formatted PDFs.

Finally, there's an extension that gives you information about how a given paper is cited in the literature. The scite.ai plugin shows you how often a paper has received approving, neutral or disputing citations.

So, overall, a fantastic collection of features that make the literature part of your academic workflow much, much easier.

Why Zotero as your reference manager instead of Mendeley?

Now, Zotero is not the only reference manager out there, of course. Endnote, Citavi and Mendeley are among its biggest competitors, and because Mendeley is also free and cross-platform is one of the main competitors to Zotero. So why choose Zotero over Mendeley?

Whether it is an issue for you that Mendeley is owned by Elsevier or not, there are three things that make me choose Zotero over Mendeley:

When you add a PDF file to Mendeley, you have no control over where it is stored. That means you can't just open up Dropbox on a friends computer and download a paper, or open up the PDF on your iPad – you need to log in to Mendeley.
That means multi-device is difficult: reading papers on your iPad or other tablet can't happen in your favorite PDF reader of choice, which means you're potentially loosing out on features.
Finally, when you highlight a PDF in Mendeley and export it, your highlights are not automatically exported with the PDF. You can still get at them, but it's much less convenient compared to Zotero, which simply points to a file on your computer and lets you mark it up with whatever app you want.

Taking these points together, I prefer Zotero over Mendeley – by a lot.

Finally, how does Zotero fit into an academic workflow?

Mostly by not being visible - you browse Google Scholar, add citations to Zotero, and then citing them while you're writing without much fuss.

What's also great, though, is that Zotero works very nicely together with Roam Research, my favorite note taking tool and fantastic companion for any academic or researcher. I've recorded a video on how I manage source metadata with Zotero and Roam, which you can watch below and have written more about here.

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