Extra

Going Further Extra Material

Since our live class time is limited, I created this section of supplementary materials for you to consult later. Here, you will find introductions to advanced features to expand your knowledge of the application. Feel free to explore the topics in whichever order you prefer!

Interaction with PDFs and Web Pages Important

Zotero features a built-in reader that allows active annotations without needing external programs.

Main Features:

• Colored Highlights: Highlight text using different colors (e.g., yellow for key concepts, red for methodology). The color scheme is preserved in the annotations section, allowing you to filter and locate specific categories of information later. (in the sidebar accessible on the left side of the PDF reader)
• Annotations (Sticky Notes): Add comments and reflections to specific paragraphs within the text.
• Image Capture: The area selection tool allows you to crop charts, tables, or figures from the PDF. The image is saved directly into your note.
• Web Page Snapshots: When you save a website that does not have a PDF, Zotero creates a local copy of the page. This guarantees offline access to the original text, even if the website changes, and lets you highlight it exactly as you would with a PDF document.

Extracting Annotations: After reading, you can consolidate all annotations into a single file:

1. Return to your library and right-click on the read article.
2. Select the option Add Note from Annotations.
3. Zotero will automatically generate a structured document. This note compiles all your highlights, retaining the colors used, comments, captured images, and page numbers for each citation.

Accessibility: Read Aloud

Zotero has a native feature to read your documents aloud. To activate it, open a file in the Zotero reader and click the headphone icon located in the top bar, just below the document tabs. Upon clicking, you can choose between three voice synthesis options. Check out the differences:

Voice Type	Requires Internet?	Multilingual Support	Notes
Standard	Yes	No	Requires a Zotero account. Usage becomes unlimited if you subscribe to one of the paid storage plans.
Premium	Yes	Yes	High-quality voices in multiple languages. Consumes a usage time quota, which can be expanded with paid plans.
Local	No (Offline)	Depends on the device	Uses your operating system’s native voice engine.

Zotero Groups: Collaborative References

To use collaborative features and cloud synchronization, the first step is to have an account linked to the application.

1. Account Creation and Setup

• Create a free account by visiting the official website (zotero.org/user/register).
• In the desktop app, go to Edit > Preferences (on Windows/Linux) or Zotero > Settings (on Mac).
• Access the Sync tab and enter your credentials. From this moment on, your references will begin syncing.

2. Managing Groups Zotero allows the creation of shared libraries to organize references and documents as a team.

• Creation and Access: Creating new groups, as well as sending and accepting invitations, is done directly through your account dashboard on the Zotero website, under the “Groups” tab.
• Group Types: Groups can be Private (accessible by invitation only) or Public (with different levels of read and edit permissions).
• Application Interface: After joining a group, a new section named Group Libraries will appear in the left sidebar of your desktop app, located right below your personal library.
• Collaboration: Members with editing permission can add articles, attach PDFs, and create notes. Every change made within this shared library is automatically updated for the rest of the team members.

Zotero Mobile: Reading on Mobile or Tablet

Zotero has official mobile applications (available for iOS and Android), allowing access to your library and reading articles away from your desktop environment.

Main Features:

• Library Syncing: When logging in with your Zotero account, your entire structure of collections, items, and tags is mirrored on your mobile device.
• Integrated Reading and Annotation: The mobile app includes a native PDF reader. Any markings, highlights, or comments made on your phone or tablet screen sync automatically with your desktop app.
• Mobile Browser Capture: You can save new references directly from your mobile browser. Simply use the operating system’s native share feature and select the Zotero app as the destination.

Storage Management: To view and highlight PDFs on mobile devices, the files need to be synchronized in the cloud. A free Zotero account provides 300 MB of storage. If your total volume of PDFs exceeds this limit, attachment file syncing will be paused. In these cases, it is necessary to purchase a storage plan or set up an alternative server, such as WebDAV.

Community Plugins

Zotero is open source, allowing third-party developers to create extensions (plugins) to add new features to the program.

How to Install:

1. Download the plugin file (usually with a .xpi extension) from the developer’s repository (such as GitHub).
2. In Zotero, go to Tools > Plugins.
3. Click the gear icon in the top right corner and select Install Add-on From File….
4. Select the downloaded .xpi file and restart Zotero.

Popular Examples:

• Better BibTeX: Fundamental for those who write using LaTeX or Markdown (such as in Obsidian), improving citation key generation and stability.
• ZotMoov or Attanger: To automatically move and link your PDFs to a folder on your computer, outside Zotero’s storage.

The old ZotFile no longer works

Many tutorials online still recommend ZotFile. Avoid it: it has not been maintained since 2022 and is incompatible with Zotero 7 or later — the author himself confirms this on the project page.

Both things it used to do are now built into Zotero:

• Renaming files: right-click the attachment and choose Rename File from Parent Metadata.
• Extracting annotations: use Add Note from Annotations, as shown at the top of this page.

WebDAV: Alternative Storage

Zotero’s free tier for attachment storage (PDFs) is only 300 MB. An excellent free, official alternative to expand this limit is setting up a WebDAV server.

WebDAV is a file transfer protocol natively supported by Zotero. In practice, this means you can connect your library to alternative cloud storage services to save heavy PDFs, saving space on your main account.

There are several storage options on the market supporting this technology. To exemplify setup, below is a step-by-step guide using Koofr, which is one of the services natively supporting WebDAV for free and reliably.

Step-by-step: Setting up Koofr in Zotero

1. Create a Zotero Account
If you haven’t already, sign up for a free account at Zotero.org.

2. Create a Koofr Account
Next, create your cloud storage account at Koofr.

3. Generate an App Password in Koofr (Required)
For security reasons, Koofr requires a dedicated app password specifically for Zotero:

• Log in to your Koofr account via your web browser.
• Navigate to Preferences > Password.
• Scroll down to the App Passwords section.
• Type Zotero into the name field and click Generate.
• Copy the generated password (you will need it for the next step).

4. Connect Koofr to Zotero
Now, configure Zotero to sync your files using your new Koofr storage:

• Open Zotero and go to your Sync settings.
• Under the File Syncing section, change the sync option from Zotero to WebDAV.
• Set the URL: Zotero already provides https:// in the dropdown box. In the text field next to it, type exactly: app.koofr.net/dav/Koofr
• Enter your Koofr email address.
• Paste the App Password you generated in Step 3 into the password field (Note: Do not use your standard Koofr login password).
• Click Verify Server.
• When prompted, confirm the creation of the zotero folder.

You’re all set!

Physical Backup on a USB Drive

You can also save everything to a USB flash drive! Since we’ve already covered how to export, simply export your entire library to your flash drive and you’ll have a secure, physical backup of all your references.

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