From CUNY Academic Commons

Many students are interested in ways of integrating citation managers, PDF annotators and cloud storage to create a research workflow. This will allow you to send PDF files back and forth from your citation manager to your tablet for annotation and archival. Though there is no universal, perfect working solution, your preferred software and devices will dictate which method works best for you. We encourage others to add their methods and tips here too.    

Here we outline research management system using the free software Zotero, Zotfile, Dropbox (2 GB free), and GoodReader ($4.99). 


Zotero basics

Getting Started

  • First, create an account on Zotero, and download the Zotero firefox plugin (or standalone platform if you prefer).
  • Restart Firefox.
  • Open the Zotero plugin by clicking on the ‘Z’ or ‘Zotero’ in the bottom right corner of the window.
  • Sync your Zotero account by clicking the gear icon (third from the left), selecting preferences/sync and then entering your account info. If sync doesn’t begin automatically, click the circle arrow, second icon from the right.
  • Add PDF Indexing software by going to Preferences, Search and installing. (This allows the text within the PDF to be searchable. You can build the entire index in the preferences as well.)
  • You’re ready to add citations!

Adding Citations

Zotero allows you to easily input citations while browsing the web.  When Zotero recognizes citation information, an icon will show up on the right side of the URL window.  By clicking it, Zotero will automatically input citation information into your Zotero account. If a collections folder is highlighted, the citation will go into that folder.  Popular sites that Zotero usually recognizes are JSTOR, Wiki, Amazon, NYTimes and Google Scholar. 

Check out the other icons on the top area of the Zotero frame.  These will allow you add citations in different ways.  You can add citations by identifiers such as ISBN, DOI or PubMed ID.  This may take a minute to load but usually works.  You can also add websites through ‘snapshots’ that will preserve the websites content for future reference or manually add the citation.

Read more:

Adding personal PDF collection

You can add your personal PDF collection by dragging and dropping multiple PDF files into the Zotero frame.  Right click on the items and request “retrieve meta data” which will enable Zotero to automatically search for the metadata and create a citation.  Note that dragging and dropping files will not remove them from their initial location.

Adding content from a tablet or phone

On your web browser create a bookmark to any random page. Title it, ‘Save to Zotero.’ Go back and edit the link by pasting in a code.  For iPhones or iPads, use:


For other tablets and devices see:

MS Word Plugin

  • Go to preferences/cite and install Word Processor Plugin
  • Look for icon in menu bar that will enable you to add citations and bibliography directly from MS Word.  Also supports OpenOffice and OfficeLibre. 

Using Cloud Storage with Zotero

Integrating Zotfile, GoodReader, Zotero and Dropbox

Dropbox set up

  • Install dropbox on computer and set up account:
  • Create a zotero folder on dropbox.  We’ll call it “zotero.”
  • For access to your Dropbox folder on a Graduate Center Windows computer, you can install DropboxPortableAHK in your network folder (U drive). Unfortunately this isn’t available on Macs.

Zotfile set up

  • Download Zotfile plugin or for Standalone (for standalone right click the plugin link and save file.  Then go to Tools in the menu bar of Zotero, add ons.  Click on the gear in the upper right corner and choose “install add on from file,” and select the file you’ve just downloaded.
  • Go to extensions, activate Zotfile, and restart.
  • Go to Zotfile preferences in Zotero (by clicking on the gear).  Go to tablet settings.  Choose your Dropbox Zotero folder you’ve just created..

Goodreader set up

  • Download Goodreader on your iPhone or iPad.
  • Sync Goodreader to your zotero folder by selecting “add server.” Add your dropbox account.
  •  Click on the server icon and select your ‘zotero’ folder. There should be an option to sync.

Sending PDF to phone or tablet

  • Go to the pdf you want to annotate in your Zotero library.
  •  Right click and select Manage Attachments/Send to tablet.
  • Select sync in Goodreader. Open your Zotero Dropbox folder.
  • Make annotations. Select sync again.
  • Back in Zotero library, right click on item and select Manage Attachments/Get from tablet
  • Enjoy your annotated pdf with notes and highlighted text.

Other resources

Here are links that go over these steps in more detail, including working with ZotPad, a filemanager for Zotero use on one’s ipad. Thanks to Sociology Cafe for the links!