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Citation Management with Zotero — ZotFile

Learn to use Zotero, a free, open-source citation management tool.

On this page:

  • What Is ZotFile? 
  • How Do I Install ZotFile? 
  • Using OneDrive for Free Cloud Storage 
  • How Do I Set Up ZotFile and Zotero to Save to a Different Cloud Storage Location? 
  • How Do I Automatically Rename New Files in a Standardized Way? 
  • How Do I Extract Annotations from PDFs? 
  • Further Help With ZotFile 

What Is ZotFile?

ZotFile is a Zotero plugin that comes with these useful features (among others):

  • Standardizes your file naming conventions
  • Changes the destination folder of your Zotero files to the location of your choice
  • Extracts your annotations from PDF files

How Do I Install ZotFile?

To install ZotFile:

  1. Go to the ZotFile web site.
  2. Save the .xpi file to your computer.
  3. Open the Zotero Standalone client.
  4. In the Tools menu, select Add-ons.
  5. Click the gear icon and choose "Install add-on from file."
  6. Locate and select the .xpi file you just downloaded.
  7. Restart Zotero.

Using OneDrive for Free Cloud Storage

As a UConn user, you have access to OneDrive, a Microsoft Office 365 app that gives you 5TB (that's a lot) of cloud storage. To use OneDrive to store all your Zotero library digital files at no cost to you, you'll need to start by setting up OneDrive on your computer.

Follow the instructions at the link below:

Once you've set up OneDrive, you need to set up a folder for your Zotero files:

  1. Click on the OneDrive icon, which is a little blue cloud, in the far right of your system tray.
  2. Click Open Folder.
  3. Create a folder within OneDrive for your Zotero files. You can name it whatever you want, but Zotero is a good choice, for simplicity's sake.
  4. Close your OneDrive folder.

Check that your new folder is regularly syncing:

  1. Right-click on the OneDrive icon.
  2. Choose Settings.
  3. When Settings opens, you'll be on the Account tab. Click on Choose Folders in the "location is syncing" area.
  4. Make sure your Zotero folder, whatever you called it, is checked. 
  5. Click OK to save your sync options, the OK to save and exit Settings.

The next steps to having your files stored in OneDrive are in the ZotFile and Zotero settings.

How Do I Set Up ZotFile and Zotero to Save to a Different Cloud Storage Location?

Set a new location for stored digital files

ZotFile can store your digital files in a location of your choice. This means that if you already use a cloud storage solution, you won't need to worry about using up your free space on Zotero's servers.

To change your file storage location:

  1. In the place on your computer where your cloud storage lives, such as your OneDrive or Dropbox folder, create a new subfolder for your Zotero files (you may have already done this, if you followed the OneDrive setup instructions above).
  2. In the Zotero client, go to Tools → ZotFile Preferences.
  3. Make sure you're in the General Settings tab
  4. In the Source Folder for Attaching New Files section, choose a folder where new attachments will go. Your Downloads folder is a good choice.
  5. In the Location of Files section, select Custom Location, and choose the cloud storage folder you created in step 1.
  6. Click OK to save your preferences.

Stop syncing to Zotero Cloud

Now that you're storing your files elsewhere, you'll want to make sure your digital files stop syncing to the Zotero cloud storage.

To changing your syncing options:

  1. In the Zotero client, go to Preferences.
  2. Choose the Sync tab.
  3. Under the File Syncing section, uncheck "Sync attachment files in My Library using Zotero."
  4. Switch to the Advanced tab.
  5. Under the Files and Folders section, in the Linked Attachment Base Directory area, choose as your Base Directory the same cloud storage folder you used for step 5 above (to change your file storage location).
  6. Do NOT change the path in the Data Directory Location. It should still be Default.
  7. Click OK to save your preferences.

Rename and move existing files

This step is necessary if you already have digital files in your Zotero library and want them to be renamed and moved to the same location as any future files.

To rename and move existing files:

  1. Sort your Zotero library using the paperclip icon, so all the references with attachments are at the top.
  2. Select all the references with attachments.
  3. Right-click on the selected files.
  4. Choose Manage Attachments → Rename Attachments.

This should both rename those files and move them to your new preferred location.

How Do I Automatically Rename New Files in a Standardized Way?

ZotFile can automatically rename digital files, like article PDFs, based on their citation data.

To set this up for new files:

  1. In the Zotero client, go to Tools → ZotFile Preferences.
  2. Go to the Renaming Rules tab.
  3. ZotFile uses codes to rename files. A typical set-up might be {%a_}{%y_}{%t} which translates to author/s last name/s_year_title. You can set preferences such as the number of authors and number of title characters lower down in the Renaming Rules tab. For other filename options, see the ZotFile offical page link below

How Do I Extract Annotations from PDFs?

To export your annotations, including sticky notes and highlights, to a Zotero note:

  1. Open a PDF from Zotero and make any desired annotations.
  2. Save the file (overwrite the original for the most seamless experience).
  3. In Zotero, right-click the PDF and choose Manage Attachments → Extract Annotations.

The annotations should appear in a note attached to the parent item.

Your experience may vary, but Adobe Acrobat Reader can be inconsistent in highlighting, which means extracted annotations may not be exact. Try Foxit PDF Reader, another free PDF reading tool, if you experience this issue.

Further Help With ZotFile