Managing references for research

Alex Hollingsworth
8 January 2021

When I was a student I was always shocked at how long it took to create a formatted bibliography after finishing a paper. This was a task that I dreaded and usually left for the last minute. As I continued on as a graduate student, I learned about the wonders of Latex, which with the natbib package and a .bib file containing formatted citation data—both of which we will discuss later on—can automatically create a bibliography for you.

While this was quite the time saver, it still meant that for every paper I had to maintain a .bib file with all of the correct and up-to-date reference material. This was in addition to saving and managing the pdf copies of papers I was citing. This material quickly became scattered across my computer. In short, this was a chaotic, disorganized approach that was laborious, error prone, and not conducive to coauthoring or working across multiple machines.

Organizing this chaos and is where reference managers shine. Think of a reference manager as a nerdy version of iTunes. It’s a single place where you can put all of your documents, organize/update metadata (e.g., authors, journal, year, title), and create custom “playlists” (i.e., folders) for each project you’re working on without physically duplicating any material. Most reference managers will synchronize across multiple machines and allow for sharing with coauthors. And many reference managers will capture annotations as well as other material (e.g., an appendix).

This article will outline one approach to setting up the free reference manager Zotero that can be easily integrated with Latex. While I use Latex and Zotero, there are of course other (and likely better) workflows. Certainly a similar set-up can be created using many different software combinations (e.g., Microsoft Word + EndNote). This is only meant as an introduction to see what’s possible. With the goal of reducing the cost of writing and producing research papers.

You can find links to the remaining content below in case you want to jump around.

  1. Choosing a reference manager
  2. Setting up Zotero
    A. Downloading and installing
    B. Zotfile
    C. Better Bibtex
  3. Importing your first paper
  4. Adding and extracting annotations
  5. Making a formatted bibliography file
  6. Using a formatted bibliography file with Latex

Choosing a reference manager

A goal of this article is to outline a free method of managing your references. Not necessarily the best method. So the first requirement is that the reference manger be freely available. Second, since I use Latex to write papers, another requirement is that the reference manager can quickly produce a .bib file that works well with Latex’s natbib package. Third, I’d like to be able to synchronize highlights and notes on pdfs across multiple machines. Fourth, I use an iPad with an Apple Pencil so I’d like to access and annotate pdfs as seamlessly as possible on this device.

The best manager I know of that meets these criteria is Zotero. Zotero is freely available, open source, cross-platform, and offers free (up to 300 MB) synchronization and collaboration. When coupled with two plug-ins, it meets all of my reference manager needs. It even has a Microsoft Word plug-in. As such it will be the focus of this article. But before we dive into it it’s worth it to list other alternatives.

You can find a more complete list of alternative reference managers here, but the some contenders are BibDesk, Mendeley, EndNote, RefWorks, Paperpile, and Papers. Some of these cost money, some are not cross-platform, and others do not allow for the simple export of annotations on pdfs. I used Papers for a long time, followed by Mendeley, but I’ve recently shifted towards Zotero due to recent changes to Mendeley’s software. Many of these other managers have fantastic features that may not available in Zotero. For example, Paperpile integrates really well with Google Docs. So if you use Google Docs as your primary way of writing, this may be the reference manager for you.

Setting up Zotero on a desktop

Setting up Zotero is quite simple and involves four simple steps.

  1. First: Download Zotero on your computer using this link.

  2. Follow the instructions on your machine to install Zotero. Once you’re done, open the program. It should look like this.

    The left pane is your file manager, the middle pane will show your files (which is blank since we haven’t imported any files yet), and the right pane shows the metadata for a selected file (again blank until we import something).

    You should also register with Zotero using your email account. This will give you access to your synchronized files online or on other machines that you’re logged into. We’re going to skip this step here and get Zotero set up on our machine.

    Before importing documents. We’re going to add two “add-ons” that will greatly improve our experience.

  3. Install and configure the zotfile add-on.

    The zotfile add-on will allow you to automatically rename files, extract annotations, and manage pdfs on a tablet.

    Go to http://zotfile.com and click the download button. Follow the instructions and download the .xpi file onto your computer.

    After you’ve downloaded the .xpi file. You’ll need to install it into Zotero. Do this by clicking Tools -> Add-ons

    In the resulting screen, click the right gear in the top-right and select Install Add-on From File. Then navigate to the location where you downloaded the .xpi file and select it. You will then need to restart Zotero.

    Once you restart Zotero, you will be able to configure your preferences related to renaming and tablet import/export in the Tools -> ZotFile Preferences menu.

    Select preference and then set-up your file naming preferences. Be sure to select Use Zotero to Rename.

    Next, navigate to the Tablet Settings. Be sure to select Use ZotFile to send and get files from tablet and to select a folder that is available on your table. I use iCloudDrive to sync with my iPad so I sync to a folder I’ve placed there called zotero. You could use Dropbox, Google Drive or anything else.

  4. Install and configure the better bibtex add-on.

The better bibtex add on allows you to make your own text citation keys. This is really nice since often these keys are not identifiable solely by their text (e.g., they may be a DOI number or a random string of text). That is, using something like ruhmRecessionsHealth2000 to identify a citation within a text is much better than DOI:10.1162/003355300554872.

Go to the better bibtex add-on homepage here.