• Phuong

PhD Tools: Using a Reference Manager to Organize Your Literature Reviews


I have to admit--reading science papers is something that I (more often than not) prioritize last. Ayumi posted last week about a marathon-esque training routine to motivate her into reading science papers, and I have also been working through it! But then I encountered a problem--I was suddenly lost in a sea of papers, and I didn’t have a good way of organizing my thoughts or notes. Have I read this paper already? What was this paper about again? What are some key words from this research that I can use? These questions became common for me. I didn’t read nearly as many papers in undergrad, and I never really took the time to figure out how to best organize my papers.


Ack so many papers!! You know the feeling.


I promise you will also find yourself in a similar position when starting to read more journal articles in grad school. Truth is, you might even go through different phases of trying out different tactics until you find one that works for you. I certainly did. I have tried creating folders on Google Drive to separate papers I’ve read to those I haven’t. I have tried to keep a physical notebook with lists and summaries of what I’ve read. I have tried to keep a Powerpoint slide deck of papers I have read and summaries for each one.


But I would always run into a problem that made these methods difficult for me to maintain. It became frustrating to download every paper onto my computer before uploading to Google Drive. The notebook method worked for a bit, but then it was hard for me to easily search and filter through my notes when I needed to look for a specific method or result. Plus I couldn’t include figures in my notebook (and I wasn’t about to hand-draw them!). The Powerpoint method worked for awhile, but I found it difficult to search for key terms and it was difficult to categorize my notes once I’ve already put them in slide-format.


And in comes Zotero to save the day! Zotero is a reference manager, and there are several other reference managers you might have heard of: Mendeley, EndNote, RefNotes to name a few.


This was taken from the UW Library webpage and is a great comparison between three popular reference managers.


I prefer using Zotero because it allows me to:

  1. Download papers directly from Google Scholar via a handy extension

  2. Attach notes and annotate papers directly online

  3. Tag papers with keywords to easily search for them

  4. Generate citations for papers within Google Docs and Microsoft Office

  5. Organize my papers into categorical folders

  6. Group related papers together

  7. Generate bibliographies and reference lists easily


A glimpse into my Zotero library. As you can see, I can organize my papers into categories on the left. On the right side is the metadata for the paper as well as personal notes and tags I can add to my papers.


This system works well for me because I can keep track of all of my papers on one platform rather than spread out across multiple folders on my computer. My Zotero library is also accessible online, so I can access the papers I’ve saved even when I’m not on my personal computer. A huge factor that prompted me to start using a reference manager was the ease with citing sources and generating bibliographies/reference lists. Reference managers save all of the metadata from a paper that you save into your library and can generate a quick citation for you with a click of a button! Reference managers are able to generate citations from a variety of different formats, so I’ve found that this was much easier for me than having to keep track of citations by hand. Think of how long this would take if you were to cite everything by hand for your 80 page thesis!! And what if you had to re-number a citation on page 50 that might mess up the numbering for the other 49 pages?! I don’t know about you, but that sounds like a nightmare! Luckily, reference managers make it easier for you by automatically renumbering all the citations for you. Whew. That’s one less thing to worry about.


It’s perfectly normal (and also encouraged) to try out several methods of literature record-keeping before finding the right one for you. Who knows, I might move away from Zotero later, but for now this has been working well for me. I encourage you to check out a reference manager to manage your literature (and life, if I’m being honest) if you haven’t already!