How to Turn Zotero into Your Ultimate Reference Manager

If you’re juggling research papers, citation styles, and tons of PDFs, Zotero can be your best friend. Not only does it help you manage citations and references like a pro, it also makes it surprisingly easy to share links to PDFs directly from your desktop library. In this post, we’ll walk through the steps of installing Zotero, setting up the browser and Word connectors, and enabling a nifty feature that lets you send online links to PDFs right from Zotero Desktop. By the end, you’ll feel confident navigating Zotero, sharing resources, and taking advantage of powerful plugins that make reference management smoother than ever. 

What We’ll Cover Today: 

1. Installing Zotero and the Browser Connector: We’ll get Zotero up and running on your machine and configure it so you can easily send items and webpages to your library. 

1. Setting Up the Word Plugin: This will allow you to insert citations and build bibliographies directly in Microsoft Word. 

1. Link-Sharing from Zotero Desktop: With the help of a plugin and a few tweaks, we’ll show you how to generate online links to PDFs from your desktop library—making it easy to quickly share references with colleagues who have access to the same group library. 

Let’s dive in! 

1. Getting Started with Zotero 

Download and Install Zotero 7 

First things first, head over to Zotero’s website and download the latest version (Zotero 7). Install it as you would any other program. 

Sign Into Your Zotero Account 

If you don’t already have one, create a Zotero account. Once you’re signed in, check your email. You’ll need to access to a shared group library to use the article sharing features, so make sure that anyone you want to share articles with has access to the same group library. 

Install the Browser Connector 

From Zotero Desktop, go to Tools > Install Browser Connector. After this, switch to your preferred browser (Chrome, Firefox, or Safari) and complete the connector installation. Once it’s installed, “pin” the connector to your browser’s toolbar so you can easily access it. Remember, the connector only works when Zotero Desktop is running, so keep Zotero open while you’re browsing. With the connector in place, you can seamlessly send files, websites, and other references to your Zotero library and organize them into folders. 

A Quick Note: Always work with the Desktop App rather than the online interface when you can—it’s just better at searching and managing your entire library. 

2. Integrating Zotero with Microsoft Word 

Now let’s get Zotero working side-by-side with Microsoft Word. 

Install the Zotero Word Plugin 

Go to Zotero Desktop > Tools > Add-ons > Word Processors (instructions can vary slightly by version). If it’s not installed automatically, follow the prompts to add the plugin. Once it’s set up, you’ll see a Zotero tab in Word that lets you insert citations, footnotes, and bibliographies with a few clicks. It makes writing research papers a breeze! 

3. Sending Online Links to PDFs from Zotero Desktop 

This is where things get really cool. Zotero 7 no longer supports the old plugin that linked the desktop library to the web version directly. But don’t worry—we’ll use a tool called Actions and Tags to create a custom shortcut that copies a public-facing link to an item in your library. This lets you quickly share a reference with colleagues who have access to the same group library. 

Installing “Actions and Tags” 

1. Download the latest version of Actions and Tags. 

1. In Zotero Desktop, go to Tools > Plugins > Click the Settings Cog > Install Plugin from File and select the Actions and Tags.xpi file you just downloaded. 

1. After restarting Zotero, go to Edit > Settings > Actions and Tags and click the “plus” button to add a new action. 

Create a New Action: 

• Name: Copy Web Library URI 

• Event: None 
• Operation: Script 
• Data: Paste the following code: 

// Check if the selected item is valid 
if (!item) return "No item selected."; 
 
// Determine the library type (user or group) 
let library = item.library; 
let libraryType = library.libraryType; // 'user' or 'group' 
let libraryID = library.libraryID; // Library ID 
let itemKey = item.key; // Unique key for the item 
 
// Construct the Zotero Web Library URI 
let webUri; 
if (libraryType === "user") { 
  webUri = `https://www.zotero.org/users/${libraryID}/items/${itemKey}`; 
} else if (libraryType === "group") { 
  let groupID = Zotero.Libraries.get(libraryID).groupID; // Group ID 
  webUri = `https://www.zotero.org/groups/${groupID}/items/${itemKey}`; 
} else { 
  return "Unsupported library type."; 
} 
 
// Use clipboard helper to copy plain text (URI) 
const clipboard = new Zotero.ActionsTags.api.utils.ClipboardHelper(); 
clipboard.addText(webUri, "text/unicode"); 
clipboard.copy(); 
 
// Return the URI as a confirmation 
return `Web Library URI copied to clipboard:\n${webUri}`; 
 

• Shortcut: / (you can pick another key if you like) 

• Menu Label: Copy Web Library URL 

• Select all checkboxes for menu placement, ensure “Enabled” is checked, and hit Save. 

Click “Okay” on the dialogue box, and you’re set! 

Testing the New Feature: 

1. Select an item in your Zotero library (the citation, not the attached PDF). 
2. Press / or right-click and choose Trigger Action > Copy Web Library URI. 
3. Now paste the copied link into your web browser. If you’re logged into Zotero and have access to the shared library, you’ll go right to that item’s web page. This is perfect for quickly sharing references with team members or collaborators. 

Installing Other Powerful Plugins

Zoplicate (Duplicate File Checker): 

• Download Zoplicate 

• In Zotero, go to Tools > Plugins > Click the Settings Cog > Install Plugin from File and select the Zoplicate.xpi file. 

• Adjust settings in Edit > Settings > Zoplicate: 

• Default action: Always Ask 

• Master Item Preferences: Most Detailed 

• Check “append duplicates…” 

• With these defaults, you’ll be prompted on how to handle duplicates as they appear—great for keeping your library neat. 

Aria (AI Research Assistant): 

• Download Aria 

• Install as above: Tools > Plugins > … select aria.xpi. 

• Get an OpenAI API key (costs are minimal). 

• Go to Login - OpenAI  

• Create an account or log in  

• In the top right go to “Dashboard”  

• In the top right click the setting gear   

• On the “Billing” tab set up a payment method and add credits (You will add more funds here when they run out or “Enable auto-recharge")  

• Once the account is funded, go to the “API Keys” tab > “Create new secret key”   

• Name the key something like “Aria key” and keep all settings default  

• Copy the API key when it comes up after. Note, this is the only time you can copy this code. You will need to re-create the key if you lose it.   

• Go to Edit > Settings > Aria and paste your Open AI API key. 

• Test by selecting the Aria icon and asking it to summarize a paper. Aria can also search your library and even compare multiple papers. 

Wrapping Up 

Today’s Takeaways: 

• Zotero + Browser Connector: Allows you to save and organize references directly from your web browser. 

• Microsoft Word Plugin: Makes citing and building bibliographies a snap. 

• Actions and Tags Plugin: Lets you easily generate shareable links to items right from Zotero Desktop. 

• Zoplicate: Manage duplication in your Zotero Library 

• Aria: Leverage AI to streamline your research workflow. 

With these tools and tips, Zotero becomes much more than a reference manager—it’s a dynamic research assistant that helps you stay organized, collaborate efficiently, and share resources easily. If this post was helpful for you, please share it with your lab and community! For future insights and updates on the latest in Psychedelic Science, you can follow our lab on BlueSky: Portland Institute for Psychedelic Science (PIPS)