Summer’s Here: Time to Organize All Those Papers!


Zotero is free open-source software to help you organize your research references across multiple platforms and devices. Image is in the public domain.

The start of summer is a great time to get organized: perhaps you finally have time to focus on something other than the next problem set, or perhaps you’re too burned out from finals to do anything else productive.  Back in the good old days of undergrad, mathematics was a mysterious substance that emanated from textbooks, whiteboards, the mouths of my classmates, and occasionally, Wikipedia. Now that I’m in graduate school, more and more of what I learn comes from journal articles, which can prove difficult to organize. When I wrote my undergraduate thesis, my papers were all printed copies stored in an accordion folder, but as a graduate student reading hundreds of articles, this system is hardly practical.  Luckily, there are several reference management programs that keep track of papers you’ve read and generate bibliographies for you.  After searching through many options last winter, I finally settled on Zotero, which I highly recommend (and no, I am not being paid to write this).

I chose Zotero [zoh-TAIR-oh] because of the following features:

  • It’s free
  • It only takes one click in Chrome, Firefox, Safari etc. to download a new paper to your collection
  • You can store the actual PDFs of the papers themselves, not just the bibliographic information
  • You can write notes about each item or tag them with keywords
  • You can highlight or annotate the PDFs using another program (e.g. “Preview” on a Mac) and import these highlights/annotations into Zotero
  • If you search for a term, Zotero will look through the titles, tags, notes, and even the highlighted passages and annotations you’ve imported for all the documents in your library
  • Zotero will generate bibliographies and in-line citations in both BibTex and MS Word

In addition, Zotero lets you share your collections with others, import collections you may have already started in other software packages, and access your collections (well, the citations at least) from multiple computers.  The PDFs themselves are stored on your original machine (by default, in your “Downloads” folder), unless you choose to put them in Dropbox, OneNote, Google Drive, or some other cloud storage.  You should probably do this anyway to back them up.

My workflow so far looks like this:

  1. Search for a paper or author on Google ScholarScreenshot 2016-05-11 19.11.48
  2. Follow the link to the website of the journal article and click the Zotero button to download both the citation and, if your university can get you access to it, the PDF.  The Zotero download button circled in this picture is available for all webpages once you install the Chrome extension, which I found to be quick and painless.  Other browsers are also supported.Screenshot 2016-05-11 19.14.04
  3. The article is happily stored in Zotero.  On the left, you have the option of organizing your library into folders.  On the right, the article metadata is listed.  The menu above the metadata allows you to add notes or tags, which are then searchable.Screenshot 2016-05-11 19.15.40
  4. Using the Mac “Preview” program, I highlight and annotate the PDF.Screenshot 2016-05-11 19.16.53
  5. When I’m done, back in Zotero I extract the highlights and annotations.  I might do this once a month or so, since I can do it for many documents simultaneously. Screenshot 2016-05-11 19.17.57
  6. Extracted annotations and highlights now appear in the righthand panel.Screenshot 2016-05-11 19.18.23
  7. I can search my entire library for the word “heck,” and Zotero will find the annotations where I wrote “what the heck?”Screenshot 2016-05-11 19.19.03
  8. If you use LaTex, simply export everything to BibTex and do your bibliography and citations from there. If you need to write something in MS Word, install the Zotero extension in Word, which will allow you to add citations in just a couple clicks:Screenshot 2016-05-11 19.27.00
  9. Upon clicking Word’s “Zotero Insert Citation” button, you’ll be taken to Zotero where you easily search for the paper you want, and it will be added in whatever citation format you prefer.Screenshot 2016-05-11 19.27.48
  10. And with one more click, you can generate a bibliography.

Screenshot 2016-05-11 20.17.10

I’ve found this system extremely helpful this semester, and if you don’t have a system of your own that you like, I suggest you give it a try.  Zotero is quick to learn, and I have yet to run into any bugs.  Granted, things don’t always go as smoothly as the example above, so here’s what to do in some other situations:

  • If you just have the PDF (say, it was emailed you to) you can have Zotero extract the citation information (e.g. author, title, year) from the PDF metadata to allow you to make citations.
  • If the PDF doesn’t have any metadata encoded (perhaps you have a scanned book chapter, for instance), you can download the citation information from the internet and then attach your PDF to it.
  • As a last resort, if you can’t get the complete citation information online in a downloadable format (as is sometimes the case with books or websites), you can enter the missing information by hand.
  • Conversely, if you find the citation online but not the PDF (or if you don’t have free access to it), you can still download the citation into Zotero.  You can always add the PDF later if you get access to it.
  • The most annoying situation is when I can’t highlight or annotate the PDF (this often happens if it’s a scanned copy that was laid slightly diagonally in the scanner).  This isn’t a Zotero issue of course, but Zotero will still allow you to type notes about the document as a whole in Zotero’s own notes section, even if you don’t have a way to annotate specific passages.

Lastly, if you’re still not convinced and want to try out other reference management software, here’s a good place to begin:

Do you have a reference manager that you particularly like? Let us know in the comments below which one is your favorite and why!

About Matthew Simonson

I am a second-year Network Science doctoral student at Northeastern University in Boston. I model homophily and time-varying dynamics on social networks.
This entry was posted in Advice, Grad student life, staying organized, Uncategorized and tagged , , , . Bookmark the permalink.

8 Responses to Summer’s Here: Time to Organize All Those Papers!

  1. Wadiyo says:

    Very interesting information and detailed tutorial, how to minimize the volume of file?

    • Matthew Simonson says:

      I haven’t had any issues with file size thus far. The Zotero library file itself doesn’t take up much space, since it simply keeps track of the citations and notes. Storing all those PDFs can take up more space, so for that you might consider using OneDrive, GoogleDrive or DropBox — but of course if you want to be able to access those files from Zotero you’ll have to synch them to your hard drive. You could also use an external hard drive I suppose. At present, my 200+ PDFs live in my downloads folder, which is probably not the best longterm storage.

  2. YYC says:

    Instead of Mac, is there any such software for PC (say Windows )?

    • Matthew Simonson says:

      Zotero works on both Mac and PC, as do, I believe, most of these programs. The only thing that is Mac-specific is the PDF viewer (“Preview”) that let’s you highlight and annotate, which is an unrelated piece of software that comes on a Mac. I imagine there are similar free programs that run on windows.

      • Brian Borchers says:

        Zotero also works very well under Linux, and there IOS and Android apps that can work with Zotero as well.

  3. Kevin Jamison says:

    Thank you, this is really nice!

  4. kmhlkmfgl says:

    Note that you need ZotFile ( to extract the annotations.

  5. Smithc562 says:

    I don’t usually comment but I gotta admit thanks for the post on this great one eckadcbkcddaeege

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