Guohui's Notes

Zotero

3 min read

Zotero is a free reference manager that helps you collect, organize, cite, and share research sources. It integrates with browsers via the Zotero Connector and with word processors; it also handles PDFs, notes, and tags.

Installation

  • Desktop: Download and install from https://www.zotero.org
  • Browser connectors: Install connectors for Chrome, Firefox, and Safari to save items directly from the web
  • Optional cloud sync: Sign in to sync across devices

Getting Started

  • Create a library and add items via DOI, ISBN, URL, or by importing PDFs
  • Organize into collections and subcollections
  • Attach PDFs, add notes, and tag items for quick retrieval

Basic Workflow

  • Add sources as you read; organize with tags and notes
  • Generate citations and bibliographies in your preferred style
  • Export BibTeX for use in other tools

Cloud Sync with Dropbox

You can keep your Zotero data (the index system of papers) and files (the pdf files of papers) synchronized across devices by storing its data directory in the default folder and files directory in Dropbox (or similar cloud storage).

Setup

  1. In Zotero, Settings > Data Syncing > get a free Zotero account and link there
  2. In Zotero, Settings > File Syncing > leave everything unchecked there
  3. In Zotero: Settings > Advanced > Files and Folders > Linked Attachment Base Directory. Choose a folder in Dropbox
  4. Repeat on other devices, link the same Zotero account, and point to the same Dropbox folder.

Alternative

Use Zotero’s own cloud sync (not free) with your Zotero account — this is the officially supported method. In this case, choose Zotero as the syncing option in Step 2: Settings > File Syncing > Syncing attachment files in my library using Zotero

Quick Check

After setup, open Zotero on one machine and verify items appear on others after Dropbox finishes syncing.

Plugins/Add-ons

Zotero has a plugin ecosystem to extend functionality. You can find and install plugins from the Zotero plugins page or through the Zotero add-ons menu (Tools > Add-ons).

You could install the add-on Add-on Market for Zotero from https://github.com/syt2/zotero-addons and use it to manage/install all the other add-on’s.

Useful plugins include:

  • Better BibTeX — Generates stable, human-readable citation keys; export to BibLaTeX, JabRef formatting.
  • ZotFile — Renames and moves PDF attachments using patterns; extract annotations from PDFs.
  • Ethereal Reference — Adds a floating window that displays formatted reference info when hovering over citation keys in word processors; lets you copy citations in various styles without opening Zotero.
  • Ethereal Style — Allows you to create, customize, and manage citation styles directly within Zotero; edit existing CSL styles or build new ones with a visual editor.

Export

Better BibTeX enables exporting to BibTeX or BibLaTeX format for use in LaTeX documents.

Export to BibTeX (or BibLaTeX)

  1. Select items to export (or select a collection to export all its items).
  2. Right-click and choose Export Collections…
  3. In the dialog:
    • Select Better BibTeX as the format for BibTeX, or Better BibLaTeX for BibLaTeX.
    • Check Export Notes if you want to include Zotero notes as annotations.
    • Check Use Journal Abbreviation if preferred.
  4. Choose a location and filename (e.g., references.bib).
  5. Click OK.

Export Options

  • Better BibTeX — Standard BibTeX format with enhanced key generation.
  • Better BibLaTeX — BibLaTeX format (recommended for modern LaTeX workflows with Biber backend).

Citation Key Format

Better BibTeX auto-generates stable citation keys based on your configured pattern (e.g., AuthorYear). Keys are generated on export; you can also set them to update automatically when items change in Zotero via the Better BibTeX preferences.

Resources

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