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A Deep Dive into Zotero Plugins

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    ResearchDock Team
    Twitter

Zotero is one of the most powerful reference managers available. It is free, open source, and widely used across research disciplines. What sets Zotero apart even further is its rich plugin ecosystem. With the right plugins, Zotero can be transformed into a powerful tool for citation management, PDF organization, note extraction, and LaTeX integration.

In this tutorial, we walk through:

  • Installing Zotero and plugins

  • Using ZotFile for advanced PDF handling

  • Using Better BibTeX for LaTeX workflows

This guide is particularly helpful for researchers looking to streamline their literature workflows or write publications and theses with complex citation requirements.

Step 1: Installing Zotero and Plugins

Zotero can be downloaded here.

Once installed, plugins are added by downloading their .xpi files and installing them through Zotero's add-on manager:

  1. Open Zotero

  2. Go to Tools > Add-ons

  3. Click the gear icon and select Install Add-on From File

  4. Select the downloaded plugin file

ZotFile: Advanced PDF Management

ZotFile enhances Zotero’s built-in PDF handling capabilities. It allows for smarter file organization, custom file naming, and extraction of annotations from PDFs.

Key Features

  • Rename attachments using custom rules

  • Move files to a cloud-synced folder (e.g. Dropbox, Google Drive)

  • Extract highlights and comments from PDFs into Zotero notes

How to Install

  1. Download ZotFile from their website.

  2. Install it using the Zotero add-on manager

Configuration

After installing, go to Zotero > Preferences > ZotFile to configure:

  • Location of Files: Set a custom location (such as a synced folder)

  • Renaming Rules: Use templates like %a - %t for "Author - Title"

Extracting Annotations

Once you have annotated a PDF, right-click the item in Zotero and choose:

Manage Attachments > Extract Annotations

This creates a note within Zotero containing all highlights and comments, making it easy to review key points from your readings.

Better BibTeX: Seamless LaTeX Integration

For researchers writing in LaTeX, Better BibTeX (BBT) provides essential citation and bibliography export features.

Key Features

  • Generate consistent citation keys

  • Automatically export and update .bib files

  • Define custom citation key formats

Installation

  1. Download from here.

  2. Install using the same Zotero add-on manager

Configuration

Go to Zotero > Preferences > Better BibTeX and configure:

  • Citation key format: For example, [auth][year]_[shorttitle]

  • Export options: Enable "Keep updated" so Zotero automatically maintains a .bib file

Exporting to LaTeX

  1. Right-click a library or collection

  2. Choose Export Library

  3. Select Better BibTeX and enable "Keep updated"

Zotero will generate a .bib file that stays in sync with your library, ready for use with Overleaf or any LaTeX editor.

Tips for Advanced Users

  • Use Tags and Saved Searches to create auto-organizing reading lists

  • Use ZotFile annotations to compile a reading summary library

  • Export notes into ResearchDock to connect readings directly to your research projects

Summary

With ZotFile and Better BibTeX installed, Zotero becomes much more than a reference manager. You can manage PDFs more efficiently, extract annotations into notes, and generate clean BibTeX entries for LaTeX. These tools reduce manual work and help keep your research pipeline organized and reproducible.

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