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Managing References with Zotero

When doing research, it's not only important to read papers in the field you are working in, but also to manage references. At MItHRIL, we use Zotero to create a digital library of references that will eventually be useful for manuscript and thesis writing. Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share research. In addition to saving a citation, you can add notes and images in your Zotero library and, in many cases, automatically download PDFs.

You can use Zotero to:

  • create and organize a personal database of references;
  • import references automatically from many websites and library e-resources; and
  • format bibliographies in your papers.

Why Choose Zotero Over Another Tool, Like RefWorks or EndNote?

Your Zotero library is saved locally, and though it is possible to create a cloud space and sync your citations, doing so requires adjusting your settings on every computer you use Zotero with. If you do your research and writing mostly on one or two computers, Zotero is a great option. Zotero can also be used offline; an internet connection is not necessary to work with your Zotero library. Learning to use Zotero is easy.

Create a Zotero.org Account

Creating a Zotero.org account is not strictly necessary for using Zotero, but it is helpful for syncing libraries across collaborators and devices.

Install

Zotero and Zotero Connector

Download the installer appropriate for your operating system, and install the Zotero Connector for your browser of choice. Zotero Connector automatically senses content as you browse the web and lets you save it to Zotero with a single click.

ZotFile

ZotFile is a third-party plugin created to help you sync PDFs from your Zotero library to your (mobile) PDF reader (e.g., an iPad or Android tablet) and extract annotations from PDF files. ZotFile also provides a way to link to attachments saved in a cloud server. The ability to extract annotations from PDF files is now a built-in feature of Zotero 6.0, and that feature of ZotFile has been disabled there; it continues to work in earlier Zotero versions.

To install: on the ZotFile site, click Download to get the xpi file; in the Zotero application, go to Tools > Add-Ons; click the gear icon and choose "Install Add-on from file"; locate your downloaded xpi file and click Open.

Note: ZotFile is currently unmaintained and updates will be rare, so some ZotFile features will not work with more recent versions of Zotero.

One benefit of ZotFile is syncing PDFs along with a cloud storage service such as Google Drive, Dropbox, Box, MEGA, or Sync. At MItHRIL, we use OneDrive, as does the rest of the university.

  1. Choose a service and download its desktop sync application (e.g., OneDrive).
  2. In the syncing folder for the cloud storage service, create a new folder where your PDFs will be stored.
  3. In Zotero, go to Edit > Preferences > Sync and uncheck "Sync attachment files in My Library...".
  4. Go to Zotero Tools > ZotFile preferences > General Settings, and set the Source Folder for Attaching New Files to a desired folder (usually your Downloads folder). This is the folder ZotFile looks to when you right-click a Zotero reference and select "Add attachment from source folder." You will rarely need this if Zotero is already configured to automatically download the PDF whenever you create a reference from the browser connector (Edit > Preferences > General).
  5. Set Location of Files to "Custom Location" and point it to the folder created in step 2. Leaving "Use subfolder defined by" unchecked stores all PDFs in a single folder on the sync drive; checking the subfolder option and adding the character string /%c creates subfolders named after your Zotero collections as you add attachments.
  6. Under Advanced Settings, check "Remove special characters (diacritics) from filename."
  7. If syncing across multiple devices, set up relative paths in "Linked Attachment Base Directory" (Zotero preferences > Advanced > Files and Folders), pointing to the folder created in step 2, on each computer where you want to access the files.
  8. To move files already attached to citations in your Zotero library, sort your library on the attachments column. Before proceeding, back up your attachments by copying the storage folder from the Zotero directory on your computer. Then select all items with attachments, right-click, and choose Manage Attachments > Rename and Move. ZotFile will move the files from Zotero's storage folder to the folder specified in the preferences, and the library will show links to the files in the new location.

Once configured, using the Zotero connector to save a reference will save the attached file to your sync app folder and attach a link to the reference in the library.

Note: because PDFs are now stored outside of the Zotero directory, moving items to the trash only deletes the reference, not the PDF. To fully remove a file: right-click the link to the attachment and choose "Show File" to open the storage folder, delete the PDF there, then in Zotero right-click the reference and select "Move Item to Trash" (or press Ctrl+Delete).

Using Zotero

Using Zotero is fairly easy and intuitive. For an overview of its features and capabilities, refer to Queen's Library's guide to Zotero.