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Organizing Papers and References without Losing your Mind

In January, Ulrike Träger wrote a great PLOS ECR post describing how to stay on top of reading during graduate school. If you haven’t read it yet, go take a look, as it’s relevant for people at all career stages. As a follow up, here are a few tips on how to keep track of the papers you want to read without losing your mind.

Choose a reference manager. Sure, you can get by creating a poster or two without a reference manager, but it’s incredibly risky to cite references by hand for manuscripts and grant proposals. Choosing and using a reference manager is also a great way to track papers as you collect them, particularly because reference managers often have powerful search functions. There are many to choose from. Some are free, like Zotero and some versions of Mendeley. Others, like Papers and EndNote, are not, though some paid programs may be free through your institution. Spend some time researching which manager fits your needs, but don’t get bogged down, you can always switch later. Personally, I have transferred references from RefWorks to Zotero to Mendeley to EndNote over the past several years without much trouble.

Choose a place to keep unread papers. Whether it’s a physical folder on your desk or a virtual folder on your desktop, it’s important to have a designated place for unread papers. This folder is more than just a storage space, it should also be a reminder for you to review unread papers. It’s tempting to download papers and forget about them, falling prey to PDF alibi syndrome, wherein you fool yourself into thinking that by downloading a paper you’ve somehow read it. So, set aside some time every few weeks (on your calendar if you need to) to review papers. You won’t necessarily read each paper in detail, but you should complete a quick skim and take a few notes. Try to resist the urge to leave notes like “finish reading later.” However, if needed, consider using notes like “need to read again before citing” for papers that were skimmed particularly quickly.

Choose how to keep track of your notes. It’s a great idea to create a summary of each paper as you read it, but where do you keep this information? Some people write separate documents for each paper (e.g., using the Rhetorical Précis Format), others write nothing at all, but tag papers (virtually or physically) with key words. The exact components of your system matter less than having a system. Right now, I keep a running document with a few sentences about each paper I read. I also note whether I read it on paper or as a PDF so that I can find notes taken on the paper itself later. If I’m doing a deep read on a specific topic, I might also start another document that has in-depth summaries. I usually keep notes in Word documents, but it’s also possible to store these notes in many reference managers.

Choose how to file read papers. Again, having a system probably matters more than which system you choose. Given the interdisciplinary nature of science, it can be complex to file by topic. Therefore, I find it easiest to file papers by last name of the first author and the publication year. It’s also useful to include a few words in the file name that summarize its content. This will help you differentiate between articles written by authors with similar last names. So, for example, using this method, you might label this blog post as Breland_2017_tracking refs. I keep articles I’ve read in a folder labeled “Articles” that includes a folder for each letter of the alphabet. Therefore, I’d file this blog post in the “B” folder for Breland.

TL;DR. The goal of creating a system to organize papers and references is to be able to easily access them later. If you follow the steps above, it’s relatively easy to keep track of and use what you’ve read – if you want to find a paper, you can search for a key word in your reference manager and/or in your running document of article summaries and then find a copy of the paper in the appropriate alphabetized folder. That said, there is no right way to organize references and I’m curious about how others manage their files. Chime in through the comments and we’ll update the post with any interesting answers!


Pat Thomson (2015) PDF alibi syndrome, Patter blog. Accessed 2/27/17.

Ulrike Träger (2017) Ten tips to stay on top of your reading during grad school, PLoS ECR Community Blog.

Sample Rhetorical Précis:

Featured image available through CC0 license.

  1. im at the start of my phd and already feeling that i have a lot of literature. i am taking your notes onboard and going to spend some time to organise my files asap. thanks

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