Citation Management with Zotero

Because Zotero is open source, many users have created tools, called plugins, to customize the software. There are many plugins, of which the ones highlighted below are only a few.

Each plugin provides instructions for installation on the page where you download it.

The first step is to read the installation instructions on the plugin page. Locate the link to access the current version of the plugin. Download the .xpi file, then go to Zotero. In the Tools menu, choose Add-ons.

In the Add-ons Manager, select the gear icon and choose Install Add-on From File. Then select the .xpi file. You can also just drag and drop the .xpi file into the Add-ons Manager.

Follow any prompts to install the plugin. Once it's installed, you can access options for that plugin via the Tools menu.

It's a good idea to restart Zotero after installing a plugin.

Digital Object Identifiers, or DOIs, are unique numbers applied to many sources, including articles and book chapters. They make it easier to locate sources and are required by some citation styles. Full DOIs may be expressed in two formats: standard (sometimes called long) DOIs, and URLs containing those DOIs. shortDOIs operate like URL shorteners, so they are not full DOIs.

Zotero DOI Manager automatically modifies references as you import them. It verifies DOIs for accuracy, can be set up to obtain long DOIs or shortDOIs to replace whatever DOI is imported, and adds tags to imported items if there are problems with DOIs (including if it can't find one).

Zutilo is a great plugin if you frequently use tags, relate items, or use keyboard shortcuts. For tags, it allows you to copy, paste, or remove sets of tags from items (rather than doing so one tag at a time). When relating items, you can select multiple items and relate them all at the simultaneously, again instead of doing the process one by one. Finally, it makes keyboard shortcuts much easier to find, and allows you to set your own shortcut key combinations.

By default, Zutilo makes some of its features available via right-click on a reference; a long list of additional functions for that menu can be found in Tools ⇒ Zutilo Preferences in Zotero. That's also where all the keyboard shortcuts can be enabled and modified.

ZotFile allows you to change where your files are saved, from the zotero.org cloud storage to the location of your choice. Since many people have existing free or paid cloud storage options (such as Dropbox, Google Drive, or UConn's OneDrive, this can be a good option to save on storage costs. With ZotFile, you also have more customized options for automatically renaming file attachments.

ZotFile used to be a great option if you wanted to work with files on your mobile device and extract annotations from PDF files. iOS support and annotation extraction are now available in Zotero automatically, but if you're an Android user, you might still want to consider it for that functionality.

CAVEAT: Changing your Zotero file storage location will make your attachments into linked files. Linked files cannot be accessed via your web library on zotero.org; you'll see attachments exist, but won't be able to open them. In addition, some features of the mobile app are disabled for linked files. Consider carefully if this is the right choice for you!

Adjusting naming conventions for files & renaming existing files

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

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 last name_year_title. You can set preferences such as the number of authors and number of title characters farther down in the Renaming Rules tab.

To rename existing files in Zotero, select one or more and right-click. Choose Manage Attachments ⇒ Rename and Move. Move is only relevant if you've modified your Zotero and ZotFile preferences to change your file saving location.

Setting a new cloud location for digital files

This is a pretty complicated process, so be sure to read and follow all the steps below. When you've completed the process, your files will appear in Zotero as "linked files," with a tiny URL link superimposed over the PDF icon to the left of the attachment.

Remember, linked files can be accessed on your computer and in your new cloud storage location, but not on your zotero.org web library or on iOS.

Step 1: Before adjusting your preferences in Zotero and ZotFile

You need to have somewhere for the files to go. If you already have a cloud storage solution set up, create a folder where you'd like to send Zotero files. You can name it whatever you want, but Zotero is a good choice, for simplicity's sake.

If you'd like to use your UConn OneDrive space for cloud storage, and haven't set it up on your computer yet, follow the instructions below before adjusting any preferences in Zotero or ZotFile.

Using OneDrive for free cloud storage

As a UConn user, you have access to OneDrive, a Microsoft Office 365 app that gives you 5TB of cloud storage. To use OneDrive to store your Zotero digital files, first you need to set up the OneDrive app on your computer.

Once you've set up OneDrive, you need to create 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, then OK to save and exit Settings.

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

Step 2: Changing your cloud storage location

ZotFile preferences: set a new location for stored digital files

1. Identify the path to your new cloud storage location (such as your OneDrive folder).
2. In Zotero, go to the Tools menu and choose ZotFile Preferences.
3. You should be in the General Settings tab. Under Source Folder for Attaching New Files, use the Choose button to select a folder where new attachments will go on your computer. Your local Downloads folder is a good choice.
4. Still in General Settings, under the Location of Files section, select Custom Location and use the Choose button to select the cloud storage folder you identified in Step 1 of this workflow.
5. Save your preferences using the OK button.

Zotero preferences: stop syncing to Zotero cloud storage

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 change your syncing options:

1. In Zotero, on a PC, go to the Edit menu and choose Preferences (Windows/Linux); on a Mac, under the Zotero menu, choose Preferences.
2. Select Sync. In the File Syncing section, uncheck "Sync attachment files in My Library using Zotero."
3. Select Advanced at the top of the Preferences box and choose the Files and Folders tab.
4. Under Linked Attachment Base Directory, use the Choose button to select as your Base Directory the same cloud storage folder you used in step 4 of the ZotFile preferences modifications above.
5. Do NOT change the path in the Data Directory Location. It should still be Default.
6. Save your preferences using the OK button.

Move existing files

To move files already in Zotero to your new cloud storage location:

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 and move.

Those files will now be linked to the new location and follow your ZotFile naming conventions.